With a direct hit from either a Cat 3 or 4 hurricane it's almost guaranteed that the Queens tunnels will be under water and the bulk of Sunnyside yard will also be under water. Additionally, while the East River tunnel mouths in Manhattan would be out of the direct flooding zone, the Hudson River tunnel mouths are right on the border line and could well succumb to flooding. Especially since they are below street level and the indicated flood zones on the city maps are for street level flooding.
The Hudson River tunnels in New Jersey are certainly safe from flooding from the Hudson, since you have a mountain in the way. I'm less certain about flooding from the Meadowlands however.
You can see the predicted flood patterns for NYC on
this map. Note, this is a large 5MB file, so it will take a bit to download it.