I live in Boston too up in Allston. I rarely fish around the city however, there are a couple t accessible spots. Southy has castle hill and the Black falcon terminal is suppose to produce fish. I also have had some success around the JFK museum and Umass Boston. Your best bet is to fish small plugs, storm shads and travel light because some places require a walk. Some guys non striper fish on the charles from the locks to watertown, but you will only catch dirty carp and cat fish which isn't really my style.

Drop me a PM sometime if you want to toss a line, the city angler is a rarity these days.
P.S. No one here give me a hard time about spot burning because all these spots are pretty well known and quite frankly the city is crowded already I'm not too concerned about it being over run by fisherman