If your pension is taxable to New York and you are over the age of 59 ½ or turn 59 ½ during the tax year, you may qualify for a pension and annuity exclusion of up to $20,000. This applies to each taxpayer individually and has nothing to do with RMD, just the amount of the pension distribution, so you're correct that you should both receive the 20K exclusion if you qualify.
Here's more info from NY Dept. of Taxation.
If you're using TurboTax Online, clear your Cache and Cookies and step through the 1099-R entries in your Federal return again. If you're a NY resident, you can enter the distribution amount in Box 16 (State Distribution), to be sure it flows into your NY return, even if it's not shown on your 1099-R.
Return to the NY interview and click on 'Adjustments to Federal Income' and then check the Pension & Annuities Worksheet to see the exclusions applied properly.
@Charley Brown
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