First did the 1099-R have a NY State distribution amount shown on the form and you entered that amount into TurboTax? That of course is the source of the income showing in the NY interview.
Next, be sure that when you entered the 1099-R for the NY pension you selected a NY source for the distribution in the follow on questions. You should get the opportunity to put a "zero" in the NY distribution box in a follow on question there.
If not, then go to the state interview and continue the NY return. When you get to the "Changes to Federal Income " page, update/start the "Received Retirement Income" topic. On the next page "Edit" the 1099-R and you will have the opportunity to exclude the pension income.
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