Just come back from a trip in NE USA/Canada myself. My advise would be just to drive from New York to Niagara in one day. It is a long drive and if you are 2 drivers you can do it , the tiresome part will be getting out of NYC, so start very early. Drove through Syracuse, didn't seem very special to me. If you go to Niagara go to the Canadian side, you will have a better view and more things to do, and in general is much nicer. Don forget the maid of the mist. The best $14 you will spend
In NYC go to Rockefeller rather than Empire State Building ( no queues, and you get to see the EST).
I have heard Vermont is very nice in the autumn, maybe investigate that as a stop on your way to Boston.
Hope you pick up the hire car when you leave NYC, if not change the reservation, you will not need a car in NYC, you will not drive it, as you cannot park it anywhere- Parkings advertise $7 for the first the 30 mins as a kind of a bargain..The subway is brilliant and cheap, will get you anywhere.
Have fun