You will need to file a federal tax return and state tax returns in both New York and West Virginia. You will file him as a resident in NY, a non-resident in WV. If wages are his only source of income, he should only need the federal Form 1040EZ.
Make sure on every tax return he is marked as a dependent of someone else.
Also make sure to prepare the WV non-resident so that he can receive proper credit for state taxes withheld.
