I tried to work with the Navy on some submerged aircraft and was stonewalled by the "always retains ownership" idea. Recently someone posted some good info here on going through some sort of US Navy Historical Office. Find that post, there was some contact info in it.
A good example is the U.S.S. Dexter, a navy cutter sold to a private towing company after more than 30 years of service. The Dexter sank off Panama City, FL in 1926 and now divers are legally recovering artifacts with "U.S.S. Dexter" engraved on it.
once sold to a private company it is no longer us govt property -- but otherwize if its not been "offically" sold it us govt / navy property ---if a vessel was donated to be a "reef" I think it might be a sticky legal mess to try and remove any parts for fear of charges of destroying the artifical "reef" --- now vessels sold to private bussinesses and later lost at sea -- those wrecks most likely "offically" belong to the ships insurance co, who paid for its loss -- but it would most likely be thought of as abandoned by now by most folks esp if it site has been known for some time and no recovery op was done --frankly most of the time its simply not worth the insurance co time / money to do salvage -- so the wrecks are just left there -- these are just the type of wrecks that sports divers love to find and get a "trophy" from.