Scroll down to the bottom for my overall recommendations.
Many of the magic bars that I have visited have more detailed reviews on this blog, so try looking clicking on the "magic bar review" tag to get a list of posts with more information and photos.
Most people in Japan do not speak English. If you do not speak Japanese, many of the really funny magicians will be less funny. Most can still do magic that you will understand even if you do not speak Japanese, but the funny parts may get lost. I am told Tokyo and Osaka are better than the rest of the country when it comes to speaking English, but since no one ever speaks English to me, I cannot say for sure :-)
In Japan there are lots of magic bars (probably more than 100). A magic bar in Japan is a place that is open six or seven days per week, usually from seven or eight in the evening until at least midnight but often until four or five in the morning. Almost all places will do magic for you at the counter or table when you show up, no need to reserve in advance or show up at some special show time. Most places will do at least 30 minutes of magic, many more than an hour, for you. Some have small stages and also do stage magic. All places serve drinks, some serve food.
In Japan (and I guess most of the world), most magic props are sold in the bigger online shops nowadays. There are quite a few Japanese online magic shops, though most probably do not ship outside Japan.
There are magic shops in Japan where you can buy lots of magic props, books (almost exclusively in Japanese, though), DVDs etc. The staff can usually show you what the tricks look like if you ask.
Magic props can also be found in other shops. The chain Tokyu Hands sells all kinds of crazy things and usually has a fairly large selection of magic props. Most larger toy stores sell the Tenyo line of magic props, as do Don Quixote and Village Vanguard chains (usually in the "party goods" area). In Tokyu Hands, there are sometimes people demoing the magic props live.
Here are some magic shops in Japan:
Magic shop Magic Land, in Tokyo. A bit hard to find, as it is located in an anonymous apartment building and the sign outside is very discreet (thank Google Maps), and located in an area where there is nothing else of interest. You can often see famous magicians visit there.
Magic shop Atlantis in Sendai. Colocated with a diving shop. Very friendly.
Magic shop French Drop, famous magic shop in Osaka where you can often meet Ponta the Smith (since he works there). Also has a large online shop.
Magic Bars in Japan
From north to south, here are some of the magic bars I have visited, and a few magic bars I have not visited but that are famous.
Prices vary, with Tokyo being most expensive and smaller cities cheaper. In Tokyo, expect to pay between 6000 yen and 10000 yen (more if you order food or drink a lot). Osaka is a little cheaper, usually from 5000 yen. Sapporo, where I live, is much cheaper and 3500 yen gets you 90 minutes including all drinks.
Both Osaka and Tokyo have many more magic bars that I have not visited and that are not mentioned here. Most larger cities in Japan have at least one magic bar, so I believe there are many many more magic bars in Japan than the ones mentioned here (since I have not traveled very much in Japan).
Te to te to te [closed], this was the first magic bar I ever visited. It is now closed.
Arukana (Arcana). I have not visited this magic bar, but I have met two of the magicians that run it and they are quite nice. I have never seen them perform magic, but I am told the magic bar is fun to visit by friends who did visit.
Welcome. I have not visited, but I have met the owner. Many people I know have visited, and they all speak highly of the magic bar. Also serves cocktails of very high quality.
Magic bar Packet, small place run by a young magician I used to work with. Very technically skilled. Can also solve a Rubik’s cube in under 25 seconds without using magic.
Hey Pola, the oldest magic bar in Sapporo that is still open. Nice place with good magic and good use of music.
Trick bar Twister, the magic bar where I work. I am usually there on Fridays and Saturdays (unless my main job has me away on some business trip), and then you can see magic in English (or Swedish). There are also four other magicians working there, two of which are very good.
Magic bar Trick, the most expensive magic bar in Sapporo and the magic bar with the most magicians in Sapporo (more than 10, though the number goes up and down quite a lot). One of the magicians is arguably the best in Sapporo, so if you visit on one of the one or two days in the week when he is there, you can get some very good magic. The guy who runs the bar is also quite good, and I hear good things about one other magician too (though I have not seen him perform). The rest apparently are not that memorable, since no one who has visited seem to remember much else.
Tomarigi. The magician who runs Tomarigi used to work as a dealer, showcasing magic props in stores. This gives his magic a very different feel than the other magic bars.
Yorozuya. Very technically skilled, and if you ask him he can probably show you a very good classic pass, Ray's rise, or sliding coins up and down the arm etc.
Cocktail bar Harada. Strictly speaking not a magic bar (a normal bar), but if you say that you would like to see some magic the younger of the two Harada who work there is usually happy to show you 20 to 30 minutes of magic (unless they are very busy with the normal bar business). Not being a magic bar means it is very cheap, you only pay for what you drink (or eat). Harada also speaks English very well, so if you do not speak Japanese this is great.
Ropossa. Not a magic bar (a Japanese "snack" bar, which means a bar with women who talk to you and karaoke), but the woman who runs it does a magic show every night. She does sponge magic, spoon bending, and a three minutes magic show to music very very well (she does some other magic tricks too, but insists she is not a magician). The place also has lots of puzzles (like Rubik's cube, boxes that are difficult to open, etc.), games (board games, card games), weird and wonderful items (optical illusions, strange musical instruments, random weird stuff), and interesting customers (lots of street performers, for instance). Food (lots, if you are hungry) and drinks are included in the cheap price of 3300 yen.
Tejina-ya Sendai. Tejina-ya is a chain of magic bars in Japan. The Sendai bar is pretty new. As all Tejina-ya, they will do a stage magic show where each of the three or four magicians working that night will do one routine on stage. There will be a show when guests show up, so you do not have to go there at any particular time. They will also do some table magic for you.
Toto's Bar is also usually mentioned when people talk about which place could be "the best magic bar in Tokyo". Toto does very strong magic and is invited to perform at the Magic Castle in Hollywood one or two times per year (so try to visit Toto's Bar when Toto is not in the Magic Castle). Also has good food.
Juniji (12 o'clock) is part of a chain of magic bars in Tokyo (including Juji (10 o'clock), Hachiji (8 o'clock)). They will do a stage show (producing doves for example) whenever guests show up, even if there are only two of you and you show up at three in the morning. They also do table magic.
Joker. I visited many years ago and the master did lots of very strong tricks (more than 10 that are used as the one super finale in other places).
Surprise is famous for having many female magicians. There are usually three or four magicians working each night, and at least one or two are women.
Cuore (previously Calvados). I visited once many years ago. The owner, Kokoro, used to work in show business as something other than a magician and has a different view on magic than many other magicians which gave his magic a different feel.
Tejinaya-Shinjuku. Tejina-ya is a chain of magic bars in Japan. The Shinjuku bar is said to have some of the funniest magicians in the whole chain, and it was indeed very funny when I visited. As all Tejina-ya, they will do a stage magic show where each of the three or four magicians working that night will do one routine on stage. There will be a show when guests show up, so you do not have to go there at any particular time. They will also do some table magic for you.
Osmand has a quite large stage and when i visited the had the whole stage on fire and produced young women out of boxes. They also did table magic. Osmand is also famous for inviting great magicians from all over the world to perform at special events quite often.
Tokyo Magic O (previously Magic Bar Issey) has several young and very cool magicians (most appearing on TV from time to time too) doing young and hip magic. Very high quality table and stage magic. The stage shows have fixed times, so you have to show up at an appropriate time to see that, but they do table magic for you at any time.
Yolo is a magic bar I have not yet visited but that my magician friends speak highly of. It is pretty new and is said to have some of the best quality magic in Tokyo at the moment. May be a bit difficult to get in, possibly needing some form of invitation.
Hearts is a magic bar in Yokohama. The first time I visited the magician did very original magic, producing a Christmas tree (small plastic tree, but still) and many other interesting things. The most recent time I visited he had changed the theme to mentalism and only did mentalism. Some of it was quite interesting and original, but I thought he was more entertaining as a magician than as a mentalist.
Kanperce [closed] was a nice magic bar I visited in Yokohama where they did all kinds of magic that I have never seen in any other bar.
Momentos is a very entertaining magic bar in Nagoya. Magi Shinji, who is famous from TV in Japan as a comedy magician, works there a few days per week and he is really funny. The other two magicians I saw were also very good, and the did famous tricks in very different ways (I have never seen such an original version of the Chinese linking rings, for example).
Triangle is a magic bar I have not visited but that is quite famous. The main star Shinichi Maruyama is extremely good technically.
Move is a bar I visited once where the man who runs it does some quite original stuff. He had lots of paddle tricks that he created himself, for example.
Tejinaya-Sannnomiya. Another Tejina-ya place. Tejina-ya is a chain of magic bars in Japan. As all Tejina-ya, they will do a stage magic show where each of the three or four magicians working that night will do one routine on stage. There will be a show when guests show up, so you do not have to go there at any particular time. They will also do some table magic for you.
French Drop is possibly the most famous magic bar in Osaka. The also have a magic shop in the same building, and an online shop. The bar has two or three magicians working each night, and the do close up magic at the counter and have a special show area with slightly larger magic. Many magicians want to visit to see Ponta the Smith perform, as he works there. I have never seen him in the bar, though I have met him in the shop.
A-Omoro is famous for having the magician Ars working there. He is incredibly skilled and if you can visit a day when he works (there are many magicians working in the bar, usually three magicians are there each day), it is well worth seeing him. The other magicians are usually good too.
A-Majide is the magic bar in Osaka that I have visited the most. It helps that they are open on Sundays and open until 4 or 5 in the morning, so you I can visit after work meetings finish. The magic is quite strong and fairly original, but the main selling point is just talking to the staff who are very funny.
Magic Time is run by Messieur Pierre, a Japanese magician who used to be on Japanese TV quite a lot 10 years ago. He speaks English very well. He is very funny and also very technically skilled.
Vernon's Bar has many different magicians performing. Close to Magic Time.
Ube City (Yamaguchi)
Magic bar Manbo. When I visited Ube for work, I thought there may not be any magic bars there since it is a small place, but there turned out to be a magic bar two minutes walking distance from my hotel. It also turned out to be one of the funniest magic bars I have ever visited! Highly recommended if for some reason you ever visit this part of Japan.
Fushigiya, entertaining and does some original stuff (like a chop cup routing with potato snacks).
Red Carpet, run by a guy I know. Funny. Often produces a live hamster.
Nishioka, the oldest magic bar still open in Japan. Very experienced magicians. Famous for every single magician doing the watch steal (sometimes three magicians in a row steal the same watch from the same person without being noticed).
In Tokyo, visit Half Moon (everyone thinks it is the best), Toto's Bar (if Toto is there), Tokyo Magic O (for the illusions).
In Osaka, visit French Drop if you are a magician and you are there when Ponta the Smith performs (because all magicians I have met want to see him), visit Magic Time (speaks English, very skilled, very funny), visit A-Omoro (if you are a magician and if you are there when Ars performs, because he just so super skilled), visit A-Majide (if you speak Japanese, because they are just funny to talk to).
In Sapporo, visit Trick bar Twister (when I am there, so I can meet you). Send me an e-mail and I can try to be there on any day that works for you. Send me an e-mail if you want to visit some other place and we can go together and I can translate for you. I like watching magic and any excuse to visit other places is great.
In Nagoya, visit Momentos.
If you are going to Japan but do not know where in Japan to go, go to Tokyo. It is huge and has everything.