Whether your wife’s income is taxed by New York depends on why she was paid. You originally said New York tax was withheld by mistake because your address was not updated after you moved to Virginia.
You later said she received her final wages, PTO payout, and referral bonus after she moved. Those items are all NY-source income because they were connected to her employment in New York. That is NY nonresident income.
If your wife received a combination — NY source income and mistaken withholding — then you can adjust your NY wage to claim only the NY source portion.
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