TJ's is a pizza place right next to grasshopper in allston which is just a normal pizza joint which happens to have a seperate completely vegan menue with pizzas (with great fake cheese and fake meats and real vegetables) like the buffalo chicken pizza and sausage pizza, and tons of subs and calzones and vegan cheesecake and stuff. they're pretty expensive and i'm practically putting their kids through college i eat there so much.
also buddhas in chinatown and brookline (the chinatown one used to have the better food of the 2 but that paradigm seems to have shifted and i would more readily plug the brookline one)
they're also veggie planet in harvard square but i encourage no one to go there because the people that run the place and work there are complete dicks (i won't get into it, but they are dicks enough that i have vowed never to go there again, thus further narrowing the list of vegan restaurants i can eat at)
big burrito/burrito max, not sure i heard at least one of them recently closed, not sure if both of them did, anyways they have a vegetarian burrito you can get without dairy or whatever and it's vegan
buddhas and TJ's i'd say are the best places in boston though. buddhas is pretty damn cheap for what it is too