As a non-resident, you would file IT-203 (TurboTax will do this for you). The New York City income tax is part of the New York State tax return, on lines 51 to 55 (for the most part).
TurboTax will calculate your New York City tax (presumably zero if you were a non-resident of the City or Yonkers) but will add your NYC withholding to your NYS withholding, so you should get your money back.
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