DH and I went last year! It was the best holiday either of us have ever had.
We stayed in Pod 51, which was great value. The rooms are small, but they've made great use of the space. I understand the same company has now opened a Times Square branch. We stayed in a double with ensuite, but they had rooms with e.g. a double and a single, bunk beds and a single, 2 singles, just bunk beds, etc.
If your son is interested in history or anthropology, or even science, the American Museum of Natural History is an absolute must. DH and I literally spent an entire day in it. The exhibits are absolutely fascinating, and they have special planeterium shows etc at certain times of day.
We got a pass that allowed us to choose a number of activities. Not only did this save us money, but we also got to skip queues at most attractions.
A bus tour is a must. If you do this on your first day there, you'll get a feel of how the city is laid out, and probably see some attractions that you wouldn't have thought of visiting otherwise. Actually, I believe you can get tickets for the bus tour that last for a number of days, and a lot of people seem to use this as their main source of transport, as it stops right outside all the big tourist places.
9/11 museum is incredible but sad. Just realised your son was born post 9/11 though 😵
For views - we did both Rockefeller center and Empire state building. Preferred Rockefeller, but both are worth a go.