For a start, where will you be located in Tokyo? Then, what are you looking for? Equipment? Fishes and plants? Books and magazine?
If you just want to browse and get an eye opener, go to Tokyo Sun Marine at shinozaki. They are one of the bigger ones around. You need to take a 30/40 mins train ride to get there. They are closed on Monday if I'm not mistaken.
Cheers,
Bookmarks