These are the stores I'd hit:
1. Mouradian Guitar in Winchester MA. This shop is 15 minutes north of Boston by car. Without question, the best place for price and selection in Boston.
2. Mike's Monster Guitar.
On Mass Ave in Cambridge, between Harvard and MIT. Mike likes oddball stuff, so you'll find a lot of quirky gear on the walls. But the prices are reasonable, and it's a fun place to visit. A friend of mine picked up a late 60's Precision there for $1,500 not long ago.
3. Mr. Music
in Allston. Prices are on the high side, and selection is up and down. One of the few shops that have been able to survive competing with GC.