| If you work in NY, you owe NY tax. Since you don't work in DE, you do not owe them any tax at all. Now it seems that your company has been mistakenly withholding taxes for DE rather than NY on your behalf. So you will have to file a NY State part-year resident tax form (IT-203) to determine how much tax you owe NY. You will also have to file a DE non-resident tax form so that you can get a refund of the money your payroll department has been paying them from your paycheck. It doesn't matter tat the company is headquartered in DE - you worked and lived in NY, so that's where you owe taxes. Talk to your payroll departmet and get this cleared up so you don't have the same problem in 2008.
As for deducting sales tax you paid on the car on your federal tax return - you can do that on schedule A if you itemize, but then you will not be able to deduct NY state income tax paid - you are allowed to deduct either state and local income tax OR sales tax, but not both. However, depending on your circumstance you may find that taking the standard deduction is more advantageous than itemizing. | 
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