Portsmouth Fabric (Portsmouth, NH) if you are taking either Rt 95 or Rt 1 north.
Knight's Quilt Shop in York, Maine (on Rt 1 in southern Maine). This is my DH's favorite quilt shop!
Cambridge Quilt Shop in Cambridge, MA (basically a suburb of Boston and home to Harvard and MIT)
Gather Here in Cambridge, MA
As others have mentioned...Keepsake Quilting in Centre Harbor, NH (off Rt 93). Kind of out of your way, but if you can work it in....awesome shop!
Have a wonderful trip. I lived in Boston for 30+ years, so if you have any questions, please feel free to contact me. Just so you know...Bar Harbor is very touristy and expensive, not that Boston is a cheap city (LOL). Be prepared to pay sales tax in both Massachusetts and Maine. New Hampshire has no sales tax (except on meals and lodging...they call it a "meal and lodging tax").