Joy and I had a delightful excursion to NYC together last October, thanks to my exceptionally generous sister Kelly (who lives just north of the city.) We took the train along the Hudson into Grand Central (which felt very much like home.)
We didn't spend a "Night at the Museum", but did spend an afternoon there (we didn't have to play catch with the T-Rex either) but it was a fun and educational tour.
We then proceeded to take a "Three-Hour Tour", but saw Lady Liberty instead of Gilligan. I still get goosebumps even though this was my seventh trip with a child to experience this.
The USS Intrepid (another movie location - - "National Treasures"). It is moored just to the north of Circle Line Tours (the boat ride around Manhattan that I highly recommend.)