It all depends on your unique circumstances, your deductions, and mainly your taxable income. However, please review the tax rates for both States below and hopefully these will help you to gain a better understanding of your potential State tax liabilities.
NEW YORK INDIVIDUAL TAX RATE
For the Tax Year 2008, New York State has 5 tax rate brackets, with a rate of 4.0% at the lowest end and 6.85% at the highest rate.
NEW JERSEY INDIVIDUAL TAX RATE
For the Tax Year 2008, New Jersey State has 6 tax rate brackets, with a rate of 1.4% at the lowest end and 8.97% at the highest rate.
But, beware, that if you work in New York City, you could also be subject to another layer of NYC Taxes, on top of the regular NY State Taxes. This typically can be about 1%.
Nevertheless, I don't think that the difference should be more than 3% of your Gross Income. But, the pay scale in NYC can definitely be more than 5%-10% of the NJ Pay scale. So, all in all, you would most probably come ahead working in NY.