It depends.
It sounds like you kept your domicile, or your main residence in New Jersey while you were attending school in New York. Unless you knew you were going to stay in New York, you would need to file a part-year New Jersey return and report the income earned while you were planning to return there.
If however, you knew you were going to stay in New York and you can demonstrate your intent to stay in New York after graduation, then you can file just a New York resident return.
Depending upon your answers to the questions above, if you determine you need to file two part-year resident returns, prepare the New Jersey return first and only report your 1099-Misc. income which you earned.
Then prepare your New York return using the W-2 income. Make sure not to allocate any of the 1099-Misc income to New York.
Read each question carefully in the state interview section as this will help allocate the income accordingly and ensure you only pay taxes on the income earned while a resident of each state.
**Say "Thanks" by clicking the thumb icon in a post
**Mark the post that answers your question by clicking on "Mark as Best Answer"