I moved to Maine a little over 4 years ago. In the Portland area I have found:
Moody Lords - this is a thrift/vintage and record shop. Mostly used and a great selection of all different genres.
Electric Buddhas - some new, but mostly used records. They also sell memorabilia and repair audio equipment.\
Enterprise Records - great rock and jazz selections.
Strange Maine - quintessential hole-in-the-wall record shop with stacks of everything that will scratch your digger itch!
Bull Moose - I have only been to the one in South Portland and can't say that I'm impressed, but I want to try the flagship soon.
If there are other Mainers here with tips, I'd love to hear it!