The New York Thruway is a little bit vague.
The rest areas and service centers are open 24 hours. This is what they say...
Rest Areas/Park and Ride Lots
There are conveniently located parking areas along the Thruway System where travelers are invited to stop and rest during their trips. There are emergency call boxes at these rest areas that connect directly to the Thruway Statewide Operations Center, located in the Thruway Headquarters Building.
The Thruway Authority does offer several commuter Park and Ride lots across the System. Parking at these commuter lots is posted for a maximum stay of 16 hours, and are not designated for multiple day stays. There are no overnight or long-term parking facilities on the System.
It seems to me you can stop at a service plaza to rest and they are open 24 hours to use those facilities but there are no special overnight accommodations (facilities) where you park. I assume that's a no designated parking area. You won't leave your RV unattended for very long and they say parking can be up to 16 hours which I assume is for commuters who do leave their vehicles unattended. "Stop and rest" is vague but that could mean 8 hours overnight sleeping I would think. I got to this page and stopped looking. I doubt there is specific language about parking RVs overnight.