NY uses your entire AGI to calculate your tax on NY income. It isn't, however, as bad as it appears. They calculate what your New York tax would have been if you earned everything in NY, but then prorate that tax based on how much of your income was earned in NY. The NY state tax interview will have a screen where you can allocate your non-NY income.
For example, if the NY tax on your entire 2015 income was $1200, but only 30% was earned from NY, your NY tax would be 30% of $1200 = $360.
Why do they do this? So they can tax your NY income at the highest possible tax rate, based on your entire AGI.
From the instructions for Form IT-203
Nonresident and Part-Year Resident
Income Tax Return:
You will compute a base tax as if you were a full-year
resident, then determine the percentage of your income that is
subject to New York State tax and the amount of tax apportioned
to New York State.
