In the Federal section....You need to edit the 1099-R, and enter the State distribution amount (Box 2a, if non-zero or not blank, or the box 1 $$ amount) into box 16.
Then on the follow-up page, you select the NY state Retirment source, that applies to yours. That should do it....but the box 16 value is the one that gets removed from NY Income.
The follow-up page should look something like this
(from a prior year and might have changed some)
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____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*