The standard procedure is to enter the 1099-R in TurboTax exactly as it is printed on the paper form.
Generally the additional questions you answer during the TurboTax program will fill this information at a later time. Whether or not your state actually taxes that amount is handled during the following interview questions when you select the source of your 1099-R.
After you enter your 1099-R, TurboTax will display a screen Massachusetts Special Handling About This 1099-R.
Mark the appropriate category of pension and TurboTax will not include the pension in your MA taxable income. (See the attached screenshot below. Click to enlarge.)
