It depends.
If I understand your question correctly, you have 2 W-2 forms but the only difference is the state section. As such, do the W-2 forms have the same employer and employer ID numbers?
If so, you can file it as one W-2 Form. On Boxes 15-17, you can simply select Add a state and then break out the New Jersey and New York amounts here.
You can then follow the steps outlined by Daniel above to complete your nonresident and resident state returns.
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