If you're staying in Center City, the best way to get around is on foot or by taking the PHLASH bus, which stops at all of the major museums and attractions. The subway system does not service the western section of Center City between City Hall and 30th Street Station.
Taxis are also plentiful around tourist destinations. SEPTA's commuter trains service most attractions in the Philadelphia suburbs; PATCO will get you to the Camden attractions. You'll want a car to get to the Brandywine Valley, Lancaster, and Bucks County attractions.