Hello,

I stayed in New Jersey (NJ) for the whole of 2009.
Initially, I worked for a company A in NJ (withheld NJ taxes) for the first 3 months of 2009. I then shifted to the NY office of company A and worked there in NY for 6 months (withheld NY taxes).
I then shifted to company B and worked in NY (withheld NY taxes).

I understand that I need to file NY taxes as a non resident and NJ taxes as a resident.

While filing my NY taxes, under gross income, do I need to mention the amount I earned while working in NJ for the first 3 months?

My form W-2 from company A displays the entire amount I earned (the initial 3 months in NJ and the following 6 months in NY) in box 1 of the NY state reference copy.

If I report the amount I earned across 9 months (3 months in NJ and 6 months in NY) in my NY state return, I owe significant taxes (and possibly a fine for having very less funds withheld for no fault of mine) to NY whereas if I only report the income I earned in NY (6 months), my withholding takes care of the taxes I owe.

Thanks for all help provided.

Your W2 from company A should have different amounst for NJ and NY ncome. The NJ amount should be the total amount, and the NY amount should reflect only the amount earned while commuting to NY. Talk to your payroll department and see if they will issue a corrected W2 that shows the correct NY State amount.

When you file your NY State non-resident tax return, you do indeed have to report all income for the year, but you pay tax only on the portion attributable to NY source, meaning the amount you earned as a commuter into NY. That's why it's important that your W2 reflect the amount earned as a NY commuter during those 6 months. Then, when you file your NJ return you also have to report all income, and figure a tax on the full amount, then take a credit for taxes paid to other jurisdictions (namely NY).