I would nix the day trip to NYC since you will only be in town for a few days. More than enough to see and do right in Philly. Don't miss the National Constitution Center, the new museum that has been getting lots of national press (well deserved). Old favorites include the Phila Museum of Art, the Franklin Institute science museum, the Philadelphia Zoo, Reading Terminal Market, Independence Mall, etc. Fun shops and restaurants along South Street. The Lights of Liberty tour/show is a neat nite time activity.
Take the ferry across the Delaware and visit the Adventure Aquarium and the Battleship New Jersey both in Camden, NJ. You can also take in a Camden Riversharks game, the local minor league team, at beautiful Campbell's Field.
As for hotels, it depends on your budget, of course. I'm partial to Marriott, myself. There is a Marriott, a Residence Inn and a Courtyard all in the main area of center city.
Happy to answer any questions. I would advise, though, that certain things I mentioned require advance ticketing, like the aquarium, Riversharks, possibly the Constitution Center. Google those places and see if you can order in advance.