Midyear Switch in Remote Status - Does Tax Law Follow State Business Incorporated or Nearest Location?

Background:

  • I live in New Jersey.
  • My company is incorporated in and headquartered in Wisconsin.
  • They have a number of office locations around the country, including New York.
  • I used to be an employee of the NY office.
  • As of April 1, 2024, I was made full time remote from my home in NJ (not a NY office worker working from home, my physical office location for work is listed as my home in NJ with no connection to NY).
  • At that time, they stopped taking NY taxes from my paychecks.
  • Since I did work in NY for 3 months, my W2 has NY reporting.  The tax is just for 3 months, but my full year income is listed.
  • This year (2025) they will not even be reporting my income to NY.

I know NY tax law means if you work remote in another state for a NY based company, you have to pay NY tax. However, as listed above, my company is incorporated and based in Wisconsin. NY is just one of their office locations. My accountant is telling me that it doesn't matter if they are incorporated in Wisconsin, that no matter what, I have to pay all NY tax for the full year and continue to do so going forward. I understand paying for the 3 months.  My argument is that the company is incorporated and headquartered in Wisconsin, and it should follow Wisconsin and NJ (as my location) tax law. I only happened to temporarily report to one of their offices that happened to be in NY. Another employee of my company who is a remote worker based in NJ from day 1 has never had to report anything to NY. This is why they automatically stopped taking NY tax out of my paychecks. Why would I forever be linked to NY then? That means it would have been better for them to fire me and then rehire me with NJ listed. 

 

I'm panicked because since they stopped taking taxes out, I'm going to owe NY thousands of dollars.