When entering a 1099-R that is exempt from New York State tax, in the Federal section of TurboTax you do not enter anything for box 12. Once you continue you will see a question asking Where is this Distribution From?
Pick the option for which New York State Department the distribution is from and the program will not include the distribution in your income for New York State Tax purposes.
Please see DanielV01's post for more information
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