New Jersey wages are higher than federal and New York wages because of deductions that are pre-tax for federal but taxable in New Jersey. Some examples of such deductions are Section 125 "cafeteria plan" medical insurance premiums, contributions to a retirement plan other than a 401(k), and FSA contributions. (New York wages are always the same as federal.) These amounts have to be included in the wages on your New Jersey tax return. If your New Jersey wages are not shown on your W-2, you have to enter the additional amounts in the New Jersey interview in TurboTax.
Enter your W-2 in TurboTax just as it appears on the W-2 that you got from the new employer, without a NJ line in the state section. When you get to your New Jersey return, near the beginning of the New Jersey interview you will come to a screen called "Other Wage Adjustments - W-2." That's where you enter the additional items that have to be included in New Jersey wages. You should be able to find the amounts for these items in the year-to-date section of your final pay stub for the year. If you need help identifying them, your payroll department should be able to help.
