Residents of all of the following are considered residents of New York City:
Per the New York Instructions for Form IT-201, page 12:
New York State county of residence. Enter the county in New York State where you lived on December 31, 2016. If you live in New York City, use one of the following county names:
If you live in use county Bronx Bronx Brooklyn Kings Manhattan New York Queens Queens Staten Island Richmond
If you select one of these counties and still select Did not live in the city on the Q&A screen titled New York IT-201 - New York City Residency, then you will see a Red Alert during the Review section. You will not be able to electronically file the return until this discrepancy is resolved.