I hope it was Boston and not Buffalo you wanted.
http://www.comicopia.com/Located in Kenmore Square, Comicopia has a great selection of manga.
464 Comm. Ave
Kenmore Square
Boston, MA 02215
(617) 266-4266
http://world.std.com/~myp/New England's oldest and best comic book store. Located in Harvard Square, they have a wide selection of manga and comic books.
http://www.sasugabooks.com/Japanese bookstore located in Waltham, MA. They have a wide selection of manga as well as other Japanese products.
http://www.tokyokid.com/The store is mostly devoted to anime paraphernalia! Posters, plastic models, anime music CDs, anime DVDs and video cassettes, some anime toys, and a very limited manga selection.
Harvard Square
36 JFK St. (The Garage)
Cambridge, MA 02138
Tel: (617) 661-9277
Chibi Toys
Affiliated with The Tokyo Kid, above. Plastic models, DVDs(?), and the like, all right across the hall from The Tokyo Kid. Underneath it is some kind of console game exchange shop, too.
Chibi Toys
Harvard Square
36 JFK St. (The Garage)
Cambridge, MA 02138
Tel: (617) 661-0278
Kotobukiya, Inc.
1815 Massachusetts Ave.
The Porter Exchange Building
Cambridge, MA 02140
Tel: (617) 354-6914
(Right near the Porter Square T Stop)
Kotobukiya is a grocery store that (I think) carries a reasonable selection of manga weekly magazines (they no longer carry tankoubon/compilations). Last I heard, Kotobukiya gets their weekly manga by ship, so they're a couple weeks behind Sasuga (great when you've missed an issue at Sasuga). They also have video rental (and Japanese junk food, AND onigiri rice balls!).
Tokai
It's not really anime related, but I'll mention Tokai at the instigation of a reader who suggested it. It's in the same building as Kotobukiya (above), and they have all sorts of Japanese decorations ranging from Sanrio stuff to tiny charms to small pieces of furniture. Plus some clothing I think too.
Harrison's Comics & Collectibles
252 Essex Street
Salem, MA 01970
Ph: (978) 741-0786
OK, it's not quite near Boston, but it's not a bad commute; about 30-40 minutes away during non-rush hour times. It's a large store with a big selection of Western and Japanese comics, plus videos, DVDs, some CDs, T-shirts, and plastic figures/models.