This EE savings bond interest shouldn't be taxable on your New York State Tax Return.
Make sure that it was properly entered on line 3 and not line 1 of Form 1099-INT, when entering your form into TurboTax.
You can use these instructions to get back to that entry:
It will look like this:
Click here for a guide to investment bonds.
Please feel free to come back to TurboTax Community with additional information or questions or click here for help in contacting Turbo Tax Support.