What exactly do you mean by "using" your federal AGI? Your federal AGI appears on your New York part-year resident tax return, but that doesn't mean that you are paying New York tax on all of it.
The first page of New York Form IT-203 has two columns for income. The first column is federal amounts, and the second column is New York amounts. The federal amounts on lines 1 through 19 are supposed to be the same as on your federal tax return, and include all your income. The New York column should have only the amount you earned in New York.
The way New York calculates the tax, it first calculates tax on your entire federal income, after New York adjustments. But then it applies an "income percentage" that is your New York income as a percentage of your total income. That's how it adjusts the tax based on how much of your income is taxable by New York. You can see this on page 3 of Form IT-203, on lines 45 and 46.
If line 1 of Form IT-203 in the New York column shows the amount that you earned in New York, the tax return is correct and there is nothing that needs to be changed.
