Technically, if you have absolutely NOTHING to do with the NJ office, and are strictly an employee of the NY office, then you should actually be paying taxes in NY.
This is actually one of those things that would be a toss up and could go either way with having NJ as your home office. This is a bit of a loophole, since they have a NJ office, they can make the argument that you are an employee of NJ, however since you have no connection at all to NJ office, it really should be NY it would seem.
With the above, NY would have every right to say that all of your income is earned in their state.
I would suggest going back and talk to your employer and bring up the fact that you have zero connection to NJ. Even if they don't change it, you can report all of your income to NY and NJ, which is probably the safest way to go.
It will not affect your NJ return as far as reportable income as all income is reportable to NJ since you live there. It will affect your NY wages and it would give you a bigger tax credit in NJ since you will pay more taxes in NY.
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