DS21, DS19 and myself went to NYC for 1 night last summer. We saw Aladdin on Broadway and then went to the Empire State Building. I suspected that there may be long lines at that time, so I purchased tickets ahead of time online and decided to splurge for the express pass - it was worth every penny!!! You get to bypass all of the lines on the way up AND on the way down. We estimated that it saved us close to 2 hours of waiting time. If you go at a busy time, I highly recommend the express pass - I think it was $20 extra per person. It was a magical experience for us
My guys chose not to go to the 9/11 museum and instead we went to the USS Intrepid, which we all loved! We also did the Tenement Museum, which was wonderful, but may depend on your kids ages.
Some of the unexpected things were memorable - grabbing breakfast to go at a nearby deli and sitting in a small park to eat, trying the different food trucks, etc. A fun family restaurant near Times Square is Carmines, which is family-style Italian - make reservations though! John's Pizza is also fun!
It sounds like you have a lot of great things planned!