We've sailed in/out of NYC several times. We always watch from the top deck. Takes about an hour from when you leave the dock to go under the bridge (after that, there isn't much to see). As you are sailing out, the NYC skyline is on the port side and once you are past the Freedom Tower, you can move to the starboard side to see the Statue of Liberty. You could certainly see the NYC Skyline and the Statue of Liberty from deck 4, but if you are up on the top decks you can check progress on both sides without having to walk back and forth. But you definitely want to be on the top decks when you pass under the bridge, that gives you a good sense of how close it is!
Only once have we watched on our way back in and that's because it was a port of call and not disembarkation port. On our last sailings, the captain told us the last night what times they were scheduled to pass by the major points in the morning but that was completely subject to change. We live in the area so we opted for sleep over sights but I think by time we got up, we were ahead of the schedule the captain gave anyway. So if you are going to watch while you sail in, plan on being up early and maybe adding a little time to the captain's estimates just in case.