In general, income earned in NYC by a NYC non resident is not subject to NYC income tax. They did away with nonresident NYC income tax about 20 years ago.That’s how it works with W2 employee. Did you prepare the 1065? They’re most likely is tax to NYC at the partnership level. I haven’t done a NYC business return in years.

edit: quick search found this

”All city residents' income, no matter where it is earned, is subject to New York City personal income tax. Nonresidents of New York City are not liable for New York City personal income tax. The rules regarding New York City domicile are also the same as for New York State domicile.”