I almost always use Bluebond Guitars, which is on 4th St. between Lombard and South. They do great setup and repair work, and Rich is a great guy. Another option is DiPinto Guitars' company shop on Girard Ave. (
www.dipintoguitars.com). They do excellent work, and it's a great shop to visit.
If I wanted a luthier for something like custom profiling a neck, I'd go to Tim Cloonan of Callowhill. I believe he also does setup work.