The way most states work in TurboTax (and New York is no exception), to exclude at the state level income that is taxable at the federal, you have to go through the state interview and remove those items that are not taxable in the state.
For retirement income, go through the New York state interview. You will see a number of screens talking about wages and self-employment and other income that may or may not apply to you.
Eventually, you will come to a screen entitled "Changes to Federal Income". On this screen, go down to Wage and retirement adjustments and click on "Received retirement income".
The next screen will show a table of all your 1099-Rs (retirement income). If you are eligible to do so and want to exclude one from New York state income, then edit that entry. The next screen will allow you to enter the "Portion of Distribution Taxable in New York" (which could be zero).