Employee lives in New York city is employed in a upstate New York based company the company has a ware house in New Jersey and he works over there which state whithholding taxes is being whitheld on his pay check the state of New York or the state of New Jersey?

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If he wrks in NJ and lives in NY, he will have to file tax returns for BOTH states. NY will give him a credit for the NJ taxes paid so he will not get double taxed.

You will need to wothhold from BOTH states, because the NY state tax rates are HIGHER than NJ, so the credit will NOT offset the NY state taxes entirely.