Yes, this could cost you extra because NYS will expect you to pay state income tax even if you are working remotely and live in another state. In addition, you may need to pay income taxes in the other state. Most states do not tax remote workers but states like New York and California are exceptions to this rule.
To receive a credit for the taxes paid in New York, you will prepare your NYS non-resident return first and then your resident MA return last. This way the New York State tax paid will properly be credited to your Massachusetts state return.
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