You will have to file a non-resident/part-year resident NY tax return to get a refund of the NY tax withheld by your employer. You will also have to file a VA resident tax return, and pay VA tax on the income you earned working in VA.

You are only subject to tax from your state of residence and, if applicable, any other state/s where you physically performed work. In the Personal interview, do not select "Earned money in another state in 2016."

You should prepare your non-resident tax return (NY) before your resident tax return (VA). This way, you may be able to get the NY refund in time to use it to pay your VA taxes. The state tax interviews (NY and VA) will allow you to allocate your income - all to VA, none to NY .