There was a thread about this some time ago...not sure what it is about Boston
I usually go to Skipton's which is across the street from Boston Medical Center in Roxbury. You can get there via the Orange Line to the Number 1 bus. Or the number 8 bus to South Bay, I believe.
There's also a petstore at the Stop and Shop mall in West Roxbury along the VFW Parkway called Pet Supplies Plus. Not a great selection of fish, but they sell supplies including food, medications, tank decor, and tank setups. Prices tend to be more reasonable than Skipton's. Depending on where you are located you can take the Orange Line to Forest Hills and then the Number 36 bus to the West Roxbury VA Hospital and then walk 10 minutes up the VFW to the store.
If you are closer to Chinatown/New England Medical Center you could always try Aqua World which is this semi-awful looking petstore buried deep in Chinatown. They sell a lot of koi and goldfish. Strangely, it appears that the store is half a fish store and half a dvd/vcd/cd media store for singers and artists from Hong Kong. Very weird. I've never bought from them so I can't vouch for their quality (either for the fish or the dvds). Chinatown of course is again accessible by the Orange Line (or the Red Line, or the Blue Line, if you don't mind walking a little bit). Or you could take the Silver Line there too.
Finally, I bought some fish at the Petco in Cambridge right near the Cambridge Side Galleria on First Street. Not bad for a large chain. You can get there via the Green Line if you get off at Lechmere and walk down First Street.
There are a few stores outside of the Boston area itself that I go to whenever I have access to a car, but you had specified T accessible, so I won't go into those. HTH~