I am currently trying to do something with the buoys located within the Great South Bay. You guys are correct saying it could take forever trying to find out who is responsible for the buoys in any given area. There are towns, villages, state, counties and federal areas. I found when you call and ask about buoys, you are directed to parks departments, division of highways and any other place they could send your call just to get you from thier phone extension, to someone other then that person's extension. It did take me awhile but I finally found the person within the US Coast Guard that should be able to tell you who is responsible for what buoys. He works out of Moriches station, his name is Anthony Certa contact # 631-395-4400. It did take a number of calls before he returned my calls, but found him really knowledgeable and more important, honest with his feedback as far as what he feels could be accomplished.
Good Luck