Generally speaking, as a NY resident, all of your income is taxable in NY, regardless of where it is earned. There is an exception to this for Foreign income, but that exception does not seem to apply to your circumstance. (For more information, click here, and scroll to the subheading "Resident" and the secondary subheading "Group B").
Where this income should not be taxable is in New Jersey. Since you are a nonresident of New Jersey, income earned outside of New Jersey is not taxed there. Thus, your income earned in Switzerland truly should be excluded from your New Jersey tax return, but included for your New York tax return. If your NJ company did not exclude this income on your W-2 (and it sounds like they did not), you may wish to get a printout or other documentation of the income earned while in Switzerland as compared to the income earned in New Jersey.
In the end, you end up paying essentially the same amount of total tax (because what you don't pay to NJ you instead pay to NY). However, NY could potentially allege that the portion of income claimed as taxable to New Jersey is actually not taxable there, and disallow the tax credit for taxes paid to NJ on that income.
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