Yes, you should enter the information from your 1099-R as it appears on the form, TurboTax doesn't have a place to enter the word "Exempt."
If Box 14 says "Exempt," enter $0 for state tax withheld.
Enter NY in Box 15, the state ID in Box 16, and the state distribution amount in Box 17.
Since you live in Wisconsin, TurboTax will help you apply for the correct state tax treatment during the state interview.
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