Unless you live in Queens, you should not be paying NYC taxes. Long Island is not one of the five boroughs, and you should not be liable for NYC tax.
In the NY state return interview, you want to select your NYC residency to nonresident. If a NYC tax has been calculated, it should be deducted with this entry.
If NYC tax was withheld from your paycheck, it should be included as part of your refund.
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