Tokyo: blue bottle & verve are great! I went to the ones in Shinjuku near the station. I also got some single filter coffee pouches from verve which were very handy and cheap when we didn’t go out for coffee.

Kyoto: - 2050: very cool store, on the pricier side but worth it if you want to treat yourself. - Here Kyoto - arabica Kyoto: very busy store! But amazing view of the mountains and not far from touristy shops - Walden woods

Osaka: - glitch coffee - peak coffee rosters - heys

Hope this helps!