If you’re thinking of stopping on the way along the Connecticut shore, Mystic has the Mystic Aquarium which the kids would enjoy. There is also the USS Nautilus and the submarine museum in Groton. Or, for a nice shore town, Madison is lovely. You could then stop in New Haven for lunch and have a chance at not terrible traffic into Manhattan, If your rental company offers the option, you may want to prepay fuel and then you can return empty. It will avoid having to fill up in NYC. Drop the luggage off at the hotel first before returning the car. Alternatively, you could drop the car at LGA airport (gas station nearby) and then take cab into the city. It may be cheaper. Or you could return in New Haven and take the train into the city. With the amount of time you have, I am not really sure how important flexibility is. You could take the train to New Haven and spend the night and then continue to NYC the next day. Yale has the Art Museum, Peabody Museum of Natural History, and Museum of British Art.