The plates go in the name of the city/county/"main" agency, not a sub agency of the government like NICE or the DOT. All plates for city agencies say "City of NY" and all plates for the MTA have MTA on them, whether its LIRR NYCT MTA Bus or whoever.
It's funny how at first NYCTs plates came as "City of NY" then they finally got it's a MTA not city agency and gave them MTA plates.