You can deduct $6,000 as "New York Source Portion" on your IT-203 nonresident return.
In an advisory opinion, New York said in a case where the nonresident husband worked in New York and the nonresident spouse did not work: "Such compensation is derived from or connected with the husband’s New York employment. Accordingly, the federal deduction for contributions made to the spousal IRA under section 219 of the IRC is derived from or connected with New York sources."
See: TSB-A-03(7)I:12/03:Steven J. Eller, Petition No. I030825B