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Possibly the tax calculated on NYC-1127 does not apply to you.  My topic list definitely includes that item.  You could go through New York interview again.   

"Under Section 1127 of the City Charter, if you are a City employee who lives outside the City and you were hired after January 4, 1973, as a condition of employment you agreed to pay to the City an amount equal to a City personal income tax on residents, computed and determined as if you were a resident of the City.

Section 1127 of the New York City Charter does not apply to you if you work for the Department of Education, City University of New York, District Attorneys' Offices, or New York City Housing Authority. Also, it does not apply if you are a NYC Housing Authority or Transit Police transferred into the New York Police Department.

For more information, check the NYC government's FAQs online."
 

Here's more info on Form NYC-1127, including a portal for paying online directly to nyc.gov.