>>1705400If you're in Taito there's a few great shops there like Keypon, Sansui, Trout Island, Tsuruya for fly fishing stuff.
You should also check out some of the bigger chain stores in Tokyo like Joshuya and Tackleberry. Do your research on what to invest in before you go and make the appropriate arrangements if you plan to bring bulky things like rods back with you.
If you put in the footwork and walk around Odaiba, you'll see quite a few people fishing like pic related. Google Maps and Streetview will be your best friend prior to going and when you're there.
You can ask local tackle shops about fishing spots and what is in season. There's usually someone who can speak passable english in the larger chain stores if your Japanese isn't up to par. But never be afraid to ask.
And most importantly, be considerate of the local fishing spots and clean up after yourself.