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Is it really the case that the standard deduction for New York doesn't consider the different contributing sources to federal adjusted gross income, such as earned and unearned sources?

Yes. State rules are often different from federal rules. NY standard deduction amounts are higher than the corresponding federal amounts for all filing statuses.

Also, just because the taxable grant is part of my federal AGI, does that really mean that NY "automatically" gets to tax it? I am a resident of NY, but the taxable grant is coming from the graduate school I started at in Massachusetts in Fall 2009 (where I am currently renting an apartment, but am a nonresident, at least as far as 2009 is concerned).

As a resident of NY, you are taxed by NY on your worldwide income. So, unless there is a specific exemption that makes your grant nontaxable to NY, it's taxable. I'm not aware of anything that would exclude a federally taxable grant from NY taxation, but look through the instructions for NY subtractions for confirmation.

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