The interest on U.S. savings bonds should have been reported in box 3 of a Form 1099-INT. You enter the 1099-INT in the federal income section, with the savings bond interest in box 3. Then TurboTax will put it on line 28 of Form IT-201. You don't enter it as a subtraction on the New York return, or make any other entries for it.
On the screen where you enter the 1099-INT in the federal section, check the box that says "My form has info in more than just box 1" in order to enter the amount in box 3.