It doesn't look like turbo tax is reducing my NYS AGI by the amount I received from a pension and a 401K. Has anyone else had issues with this?

If your pension is from a government agency, it is not taxable in NY.  An IRA may qualify for the $20,000 exclusion (age 59.5+) according to  Publication 36. The program will handle the $20,000 exclusion but you must enter the nontaxable retirement.

Follow these steps.

1. Log into Turbo Tax
2. Select the State  Taxes tab
3. As you navigate through the screens, you will see a screen that says Changes to Federal Income.
4. Scroll down to Wage and Retirement Adjustments
5. The first entry below that will say Received Retirement income.  
6. Start/ Edit
7. Retirement Distributions Summary, Done
8. On the screen titled Governmental Pension Exclusion enter the taxable amount to exclude from the NY return. Here is where you would enter the full amount of your retirement distribution.
9. Continue
10. The next screen will show you the Pension Deduction Summary