Thanks for these great suggestions all. I did know about McCabes and will be heading there next time I'm on the west side of town.
Larry Larson's in Glendale was good, but I actually found a great shop in Echo Park on the corner of Sunset and Alvarado. They had a nice selection of Fleas, Flukes, Mahalos, and some top of the line (read: expensive) brand I'd never heard of. Also had a full line of Boulder Creek Riptides. I played around on a concert with a pickup and boy did I want to leave the store with that thing!
Buffalo Bros is Carlsbad I knew about too from when I went to grad school in San Diego. They also had some great mandolins there. Huge store.