Massachussetts has Newbury Comics which they have franchised throughout the state. The flagship store in Boston isn't really that cool. The stores all remind me of a hastily assembled, overly-corporate combination of the modern Commander Salamander and SMASH. They took all of the annoying elements and combined them into one shop. They sell lots Doc Martens, Manic Panic, overpriced comics/dvd's, and Operation Ivy t-shirts to the overprivileged, wannabee punks. That's the closest thing that I could find in Boston resembling a cool record store.
As for the Amoeba situation, there's absolutely no such thing as low rent in SF, which rivals only NYC as the most expensive city in the country. I bet they got a long term lease or bought their turf in the Haight and Berkeley years before the Bay Area went through the tech boom. The kids who live outside the store begging for change and burritos are all rich and hate their parents. They make great coin from passersby on that corner doing their thing.