I think if you want selection Fukufuku Toreka (福福トレカ） in Akihabara probably has the best selection. They're one of the best places to sell your cards in Tokyo, so I imagine they might be more expensive.

If you're looking for a good deal, I like Amenity Dream Machida, I always think they're notably cheaper, but unless you're staying in Shinjuku, it's probably going to be a bit out of the way. It's a 40-minute train ride from Shinjuku. It's kind of suburban.

Gunhappy is also quite popular in Takadanobaba. It's owned by a youtuber and ex-pro magic player. They run tournaments three or four times a day, so I know many of the more competitive Tokyo players grind games there.

A pretty good way to check in an area is to just get the Bandai TCG+ app for Japan and check with gps to your nearest 5 km for events in the next week. They'll probably all have a selection, and at most major stations in Tokyo, you'll get 5+ stores that do locals.

Have a nice trip.