Well, to be honest I never really shopped for the best prices and quality for used CDs. But I do favor Tower Records on Broadway because I've bought a used CD at this location, the CDs always appear to be in mint condition.
Now the only complaint I have is that they're used CD selection is spread throughout the store. On all three floors you have a USED CD Section so make sure that if when your searching you look through all the sections.
Also if you call during the day during the week, the sales rep that answers the phone might be kind enough to actually look to see if they have a particular cd, which could save you subway ride.
Hope this was Helpful - Paul