When you enter this information in the federal section there is a page that asks about the source of the distribution (see screenshot). This will tell TurboTax that it is not be included in your New York income. There is one more thing you should check on the 1099R to make sure this page appears. Edit your 1099R and make sure box 13 is NY. Click continue andd you will see the screenshot page.
If you have other questions about this, ask in the comment section below.
