Along the same lines as the Courtyard, there is a Residence Inn and a Marriott right there, too. All would be convenient for the historic sites. I haven't stayed in any of them so can't recommend based on personal experience.
Sometimes you can get better deals at hotels that cater to business travelers, so I wouldn't rule out nicer hotels. Try calling them'checking websites for deals. I've liked the Ritz (in an old bank building next to City Hall), Loews, and Omni Society Hill. As a PP recommended, The Four Seasons is really nice, but not quite as convenient to sites and less likely to have deals.
I wouldn't stay in University City, and I saw this as a Philadelphia native.