USS Intrepid, One World Trade Center & 9/11 Memorial, Grand Central Terminal. Central Park.
Empire State has big queues even if you’re pre-booked, so the current advice is to go to Top Of The Rock (Rockefeller Center) instead – that way you also get to see the Empire State Building.
Make good use of the subway system, it’s pretty cheap and goes mostly everywhere. Walking across Manhattan can be a bit of a stop-start affair as you generally have to stop for traffic every block.
I’ve heard the queues for immigration at JFK can be horrendous; I flew into Newark and it was a case of “what queues “