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State tax filing
....BUT as noted in the answer above.
1) (and using a "guess" as to your exact situation) ....if you physically worked in NY part of the year, and then telecommuted from you NJ home to the NY office for the rest of the year...then NY taxes all of that income...since they do assess the tax on telecommuters, and that is what your employer should be doing.
Yes...NJ will also use the same income to calculate a NJ tax (Along with any other income you have), but NJ will then allow you to take a tax credit for the taxes that you had to pay to NY (but only up-to the tax that NJ would have applied to the same income). The tax software does that calculation, but only if you do the NY non-resident tax return first....so.. Make sure you fill out your NY non-resident tax return interview before the NJ interview....but neither NY nor NJ should be done until the Federal forms are entirely filled in...every scrap.
2) IF, on the other hand, you were reassigned to an actual physical company office in NJ for the last 3/4 of the year, then yes, the company "should" only withhold NJ taxes for that 3/4ths of the year and assign the amounts appropriately.....and you need to get that straightened out with your company ASAP if they aren't doing that yet.