My daughter goes to Harvard and basically all i found was Guitar Stop up Mass Ave. It's about a 20 min walk...we hit it on the way to get udon noodles up there at Yume Ga Akurara...I'm a sucker for udon...anyways, yeah it's a so-so shop, some starter guitars up to some decent Fender american strats and P-basses, etc.
Music Emporium is pretty much the Boston guitar store, best I can tell. Way up Mass Ave into Lexington. That and Guitar Center.