Matts in Weymouth is probably the coolest for boutique stuff. Although, (flame suit on) the GC at Fenway had a decent selection of $20k vintage strats.
Matt's Music and Crossroads in Hanover . Also, my new go to is The Music Box in Plymouth. Owner is awesome and a great selection of axes, repairs, etc.
You have Matts Music of course, tons of GC's (check the online used inventory, Boston store has friedman) Music Emporium for acoustics, performance music in woburn, King Guitar in RI, Manchester Music Mill in NH, Mooradian Guitars in Winchester always has some cool stuff. And of course Mr. Music in Allston.