Iv herd reall good things about the MIT flea market from members here, i might be checking it out as well. ill also give a vote to spinnakers, not the largest selection but worth taking a look.
there is also a store called "cheap thrills" over in dedham if your gonna be around the boston area and the guy basically sells from his collection of 40,000 LPs in closet of a store and has a wharehouse of another 50,000... he runs funny hours though so it can be hard to catch open. the prices are amazing if you see him in store, he makes all his money selling over the internet so gives crazzy discounts if your in the shop.