It has already been mentioned, but the art museum and the Rodin museum are really great.
The mummers museum is also really unique, but it isn't open every day so not sure if it will be an option for you.
Reading terminal is really nice, but the last two times I was in Philadelphia it was too crowded to get anything.
The sea port museum is fairly nice, and the adjacent park often gives you good views of visiting ships.
Cheese steak, provolone is fine, but remember to get the pepper sauce.
Food: there's a market street that is to the north of pats and genos that has an assortment of interesting stands and little restaurants.
China town, good place for food if it has gotten late. Also has a good, fairly affordable hotel if you need find a place for the night.