DMV in NY state is my worst bureaucratic nightmare, and I'm sure that they hire their employees by personality tests.  If the person is nicer than a pitbull on PCP, they won't be hired.
I feel your pain, exactly the same thing happened to me with a car, that I had inherited and was changing from a MN registration to a NY registration. It was my grandmothers 1972 Dart, it had been purchased in Utah, and when it was moved to MN registered there.  When I moved to NY, it took me three tries at the DMV, each time taking every peice of paper they said I needed, waiting more than an hour and then being told I needed something else.  I think I drove about a year with out-of-state plates.  They even wanted the original sales tax paid on the car....bought in 1972, regisistered.....wait for it.........in 1989.
The rabid, PCPed pitbull I dealt with had moles/growths all over her face, and she was incredibly nasty to me.  I came within inches of saying "with a face like your's you really should cultivate your personality".  But I'm not that mean......mind you she would have said it.
I hope you can find a way around it.  But you may have to move out of state, register it there and move back..... 
 
DMV in NY is run by Satan.