We have asked our administrative assistants for advice and they (being very knowledgeable in these matters) recommended the following hotels as affordable and generally accessible to and from campus via a bus or subway.
The Gables (a B&B)
http://www.gablesbb.com/
The Latham
http://www.lathamhotel.com/
The Club Quarters
http://www.clubquarters.com/loc_philadelphia.aspx
The Omni
http://www.omnihotels.com/FindAHotel/PhiladelphiaIndependencePark.aspx