how much time do you have there? for a quick fix, you can chechk out Tokyo tower, a whole lot of fish in a small area . ther is also Shinagawa aquarium which is more of the all day event type deal its a bit of drive, but a quicker trip by train. as far as fish stores go, ill dig up a link i have somewhere that has maps of most of the good LFS in Tokyo and the outlying areas. If you are staying in tokyo be sure to take a walking trip down Ginsa there are a few very nice stores there. be sure to check out any chainstores like kanedai or tiara's.
this post reminds me, i owe sinisterJ the same link to all the lfs. better get looking for that link now.