There are a handful of bottle shops in the city, but its currently expensive.
The Foodery is the most overpriced but has a massive selection.
The best place Ive gone to in the city as far as prices and great selection go is "Beer Heaven" on Delaware Ave (Columbus blvd). Their prices are unmatched as far as bottle shops go within city limits.
+1 for Beer Heaven. I make the trip from South Jersey to go there once in a while since it's easy to get to and the selection is pretty good. The prices at all the shops in Philly are more expensive than what I pay in Jersey but thats the trade up for selection.