TurboTax Forces Itemized or Standard Deduction on New York Return
Per New York State tax law law, if you and your spouse are filing separate New York returns, both spouses must take the same deduction, whether itemized or standard.
The couple is not allowed to "mix 'n match" the type of deduction.
Source: Instructions for Form IT-203 (2012 version), page 33.
"If you are married and filing separate returns, both of you must take the standard deduction unless both of you itemized deductions on your federal returns and both of you elect to itemize deductions on your New York returns."