Philly is great! I'd go back.
We all enjoyed touring the Eastern State Penitentiary. Kids were 7, 11, and 13 at the time. They got to try out the cell lock where Capone stayed. It was a unique experience.
We also drove over the bridge to New Jersey to tour Battleship New Jersey.
Liberty bell only takes a few minutes.
FYI- if you want to tour Independence Hall in Philly or the Statue of Liberty at all, you need to purchase tickets in advance. It's well worth scheduling your day around a tour of the crown of the Statue of Liberty if they're still available, it was awesome!
When we stayed at Liberty Harbor, we took a ferry over to NYC and right where we got off the ferry, there's a stop for the on-off tour bus. We did try the subway too, but we found the on-off bus a great way to sit back and tour NYC.
Enjoy your trip!