1) are you sure that those taxes withheld aren't lumped into box 2?   2) did you receive a form from a third party administrator, such as ComputerShare?

Yes I'm sure it isn't shown on W-2, my final pay stub has it in the "After tax deduction" section

If the compensation is on your W-2 then the withheld taxes associated with the compensation should be on there also.  Ask your payroll department.  If the taxes aren't on your W-2 - I'm betting they are - then get a corrected W-2.

If you are sure that these taxes were withheld in 2016 and not reported elsewhere, you can enter it manually.  Go to:

Click Federal Taxes (top menu)

Click Deductions & Credits (just below top menu)

Scroll down to Estimates and Other Taxes Paid and click Show More

Click Start next to Other Income Taxes

Answer Yes, then scroll down to Other Income Taxes Paid in 2016

Click Start next to Withholding not already entered on a W-2 or 1099