Generally the base of the windshield will work fine (and the top probably would too). The base of your windshield is about the same height as the top of some car windshields, after all.
I hope you at least considered enrolling in New York's motorhome plan for EZ-Pass. On the thruway, with that plan (which doesn't cost extra to be in), you pay car rates based on the number of axles rather than motorhome rates. For a two-axle motorhome with no towed vehicle, that works out to saving just about half on the tolls.