No- You cannot file a joint return for NY state if you file separate federal returns (whatever the reason).
The only exception to having the same filing status as federal is if you filed joint on federal. In some cases, you could then file separately for NY. In no case can you file separately for federal and joint for NY.
Keep in mind that, in some cases, filing separate federal returns can cost you thousands in tax savings. Make sure that the benefit of lower loan repayments is worth the separate tax returns.
For federal purposes, you either both itemize or you both take standard.
