Of the stores I listed, only three still exist.
Mr. Music is in Allston (part of Boston)
Bill's Music is in Peabody, near me bordering Salem.
Retro Music in Keene, NH
If you're in Southborough, there are a couple of shops in Worcester you could check out. Everyone says Union Music is really good. My bass player friend bought his Dan Armstrong and Jerry Jones basses there. Remedy Music in Worcester is also supposed to be pretty cool, but small.
If you venture towards Boston, Monster Mike's in Central Square, Cambridge is a nice little shop. He mostly caters to the Garage and Rockabilly crowd, so he'll have Tiescos and Gretsches. Matt's Music is to the south in Weymouth, and Performance Music is to the north in Woburn. Music Emporium is just west in Lexington.
Then, if you go west from Southborough, there are some cool shops in the Easthampton and Northampton area. Mill River, Bird House, and Luthier's Co-Op.
There are more cool shops within a couple of hours such as Friendly River Music in Hiram, Maine and Northern Lights Music in Littleton, NH. It all depends how much of a road trip you want to take.