Did you work outside of the state of NY and on the road or did you work from home for the other 43 days?
It is possible that NY will tax ALL of the income for the last 82 days of your work year due to the fact that NY has a Convenience of the Employer Rule. Basically, this rule says if you are working remotely for your convenience then you are considered to be working in NY. If you are working remotely for your employers convenience, then you would not be considered to have income from NY sources. Since your employer does have office space for you and does not require you to work from home, there is a good chance you do not meet the criteria to exclude the days working from home as NY sourced income.
If you DO meet the criteria to not be considered to have income from NY sources you would enter your NY income for the 39 days and your withholdings as however much was withheld for NY.
If you do NOT meet the criteria to be considered working remotely for the convenience of the employer, then ALL of your income would be taxable to NY. In this situation, you will file your NY return FIRST as a nonresident and include ALL the income earned in NY. This will all be taxed by NY. But you will then receive a credit on your NJ return for taxes paid to NY.
Depending on your income and situation, it may seem like double taxation as both states will tax the income, but then if your NJ tax rate is higher than your NY tax rate, then the credit for your NY taxes on your NJ return may leave you still having to pay more in taxes to NJ. Or the opposite could be the case, if your NJ rate is less than your NY rate, then the credit you receive will only cover the specific NY earned income and not give you a full credit that resulted in a refund.
NJ taxes paid to Other States
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