It is good that you saw this screen in the federal return (and I agree it could be formatted better). Did you also see the corresponding screen in the New York State interview?
In the NY interview, there is a screen with the title of "Changes to Federal Income". Under the subheading, "Wage and retirement adjustments", please click Start for "Received retirement income ".
This section of the interview gives you the chance to revisit and possibly update your information from the federal 1099-R interview for your pension.
When you have finished this (possibly you don't have to make any changes) and continued, you are asked about the LIRR pension and then you are presented with this screen, "Pension Deduction Summary".
Does your pension show as deductible here under "New York deduction for government pensions"?
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