Found this on FindLaw.com. It is for Pennsylvania but you may be in a similar situation.
"All private rights to air space over land are subject to the right of passage or flight of aircraft. "
http://knowledgebase.pub.findlaw.com...ytortlaw_2_142
I remember reading about your tree issue before. If New York has a similar definition in the homeowners right to airspace, with the same restrictions, the state would be able to use Eminent Domain to take the tree down.