Get your taxes done using TurboTax

The entries show on my side as imported from QuickBooks. I know you said you did not import QuickBooks, but had you last year? Perhaps that carried over to this year. 

The estimated payments are not listed on your state return. The payments are listed on the MCTMT worksheet. The total tax paid is on IT-203 line 66.

When you open the NY state return section, you should see "You Just Finished Your New York Return"

Click UPDATE for "Credit and Other Taxes"

The program may ask about the START credit, continue

Scroll down to "Metropolitan Commuter Transportation Mobility Tax"

Continue to the "Your MCTMT Payments"

Do you want to work on the MCTMT?   YES

Allocate the income on the next screen, but I don't think it will matter since your income is below the threshold

Continue to the "Your MCTMT Payments" screen

Your return shows the four payments all dated 2/15/2025

If they were not made, please delete or edit them on this screen

No estimated MCTMT payments results in a NY refund of 1,002 which is 301 less than the 1,303 it started at.