You'll claim your refund for NYC taxes as part of filing your New York state income tax return.
If you won't be subject to NYC tax in 2016, you might want to fill out the attached form and give it to your employer.
"New York state income tax return" is awfully vague. Could you be more specific? Form #, line #, etc...
Thanks
Since you're using the online version of TurboTax, you won't see forms until you finish and print the state return, but there will be questions in the interview concerning NYC tax. You should end up with form IT-360.1. Your tax as a part-year resident will appear on line 55 of that form. That figure transfers to line 50 on form IT-201. The NYC tax withheld appears on line 73. Basically, your state and NYC tax liabilities are combined, and your state and NYC taxes withheld are combined. In the end your state refund includes your NYC refund. There are no separate tax forms for NYC.