I agree with flash, if pressed for time, top of the rock makes more sense than the empire state. Not only is it more spacious up there allowing more time to enjoy the view without being pushed out of the way, but you can actually see the empire state.
I would argue it doesn’t really matter where you stay as once you’ve mastered the subway, getting around is very easy and the attractions are spread all over the place anyway. For what it’s worth, we stayed in the beacon hotel on the upper West side, it was Bob on for us.
Don’t stress about getting everything done, you won’t, you’ll need to go back! Just enjoy it! We were there 9 days, never stopped and there’s loads left to do.
Make sure you get breakfast in a deli/cafe and just listen to the locals.
Stuff I would do next time includes more time in Brooklyn including the brewery tour, Coney island, Harlem, USS intrepid, a friend did a walking food tour which sounded great.