What you may have is a specific situation in which the Navy pays for medical school in return for a commitment to continue service in the Navy.  Medical school requires a residency, which the military cannot provide.  So he is still in the Navy, but completing his requirement for the M.D. by working for a non-military employer.  Have you asked him, if that's what happened?  Otherwise we are all blind people trying to describe an elephant.  

If he is a resident, then he is a nonresident.  Which is to say, if the purpose for his working in a New York hospital is to complete his Navy-financed education, then he did not become a New York resident.