Ditto a lot of what TRO said. We've been to 3 Army/Navy games in Philly and have done everything on his list except the dinner cruise. Several good eateries on the river, however.
We have stayed downtown at the Crown Plaza and the Doubletree. Both are good options, and we felt safe walking around downtown at night, but of course there aren't always some 70K Army and Navy active and retired personnel in the area.
The subway system is a good option for getting around.
A couple of other attractions that I would add for you to see are the Betsy Ross home, and Christ Church. Both full of very interesting history.
Do check out Pat's and Geno's, however. It's an interesting area and the cheesesteaks are pretty danged good, and since they are right next to each other you can do an honest to goodness comparison.
And for the record, I prefer Geno's.
We enjoy Philly and we already have hotel reservations to go back this December for Army-Navy.