Harvest Records
A little heavy on the hipster tunes .. but still a good place to look for obscure music and They will actually order something for you if they can
Harvest Records | Recordings
Karmasonics
Pretty decent selection. They may be able to turn you on to some alternative bands that you wouldn't have known otherwise.
Karmasonics | Facebook
I am a firm believer in supporting small, local record stores than the big retailers. Expand your horizon and pick up a cd by a small group on an indy label