Normally any 1099R Federal amounts distributed to you are also automatically transferred to your state return, even if not shown on the 1099-R.
If you indicate that your pension is non-taxable when you enter it in your Federal return (state employee pension, for example), it will not be taxed at the state level. Check your 1099-R entry to be sure you indicated the pension source that makes it non-taxable in New York.
Otherwise, as you proceed through the NY interview, you will be able to indicate that your pension is non-taxable, or qualifies for a 20K exclusion.
Here's more info on New York Pension Income.
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