I love the Temple Emporium! Run by a nice woman who runs the shop out of the basement of her home in the woods. Definitely the most out-of-the-way pet shop you'll ever visit.
Nice fish. I think you'd have a much lower chance of introducing a disease into your tanks if you shop there. The fish have been there for weeks if not months in many cases. She had some emperor tetras there last time that were huge by pet store standards.
Also don't forget Jay's aquatics in Salem (NH) right off 93. They have a greatly expanded selection of freshwater gear and fish since my visit a few years ago. Prices not bad, and a few plants.
Loads of marine stuff. They also stock what looks like the full New Life Spectrum Line.