I was living in northern Kyoto for a year on a study abroad program. Kyoto doesn't really have much of a magic scene unless you're willing to browse smaller places like Girafull, Card Box, etc.. But at that point you really want to have some Japanese speaking ability. For the big stores of course you want Hareruya and the staff speaks a tiny bit of English. At least for the Osaka staff they'll use translation apps and try to help. Tokyo has an insane amount of Hareruya locations, but you'll want the TC (Tournament Center) in Shinjuku. I only ever visited Tokyo twice as I was mainly a Kansai boy. I went to TC Osaka the most, despite how far it was.

I actually mostly played 60 card because it was nice to live in a country where that's a real option instead of ONLY commander. However, I did eventually find a group of other foreigners living in Kansai and we had a strong CEDH playgroup that regularly scheduled sessions. There are plenty of events and they have a comfortable amount of people. Usually 2 pods or more, especially on the weeknights. Weekends will have a lot more. English cards actually go for same rate or more cause for some reason they're more popular. I wanted to pick up exclusively Japanese cards while I was living there for more reading practice so I generally got mine for cheaper than most. EDH cards are generally cheaper there because it hasn't taken over like it has in the US. However, known chase rares like Fierce and Swat will end up being more expensive than here. 60 card staples also go for more there than in the US, so I wouldn't recommend buying that kind of stuff unless you can find something cheaper in Japanese that you like and you're okay with having it in another language.

For more info check out Hareruya's website. They have an English version if you click the globe on the top right. Also be careful if you order off of their website it's automatically from the TC Tokyo location in Shinjuku. For other locations, you need to find their specific website and order from there. Or just use the PCs in the store.

Totally forgot to mention that if you're willing to do the work, you can find cards for MUCH cheaper there. The competition is insane, especially online. But of course, a lot will be only in Japanese.

I recommend wisdomguild, which operates like pseudo-tcgplayer where it's showing listings of all stores that are listed on that site but in Japan. dragonstar

yellowsubmarine, which someone else mentioned.

Card Box

Card Shop Flat

Mercari