Portsmouth Fabrics is on Penhallow, right downtown. They do a lot of modern fabrics, batiks, and Kaffe Fassett. The shop is small but packed full. Keepsake Quilting is about an hour and a half away, and it's not to be missed.
I am sorry to disagree, but Marden's seems like a real dive to me. If you are accustomed to paying a high rate per yard, though, it could be worth a trip. The store is huge, selling all sorts of things, but it is dirty and has smelled bad both times I've been there. I'd wash anything you buy there before putting it in your suitcase.
People say good things about Quilted Threads in Henneker, NH, and there's also a shop called Golden Gese in Concord. Sounds like a few excellent road trips to me!
hugs,
Charlotte