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Yes, the income limitation of $100,000 excludes any 401(k) contributions you make because those amounts are subtracted from your income for both federal and state income tax purposes. Hence, the state income tax box on your W-2 will be reduced by the amount you contribute to a 401(k). The amount from this box is entered on line 14 of the NJ 1040 which is part of the taxable income amount on line 26 used to determine the eligibility for the pension exclusion on line 27a.
See page 27 - http://www.state.nj.us/treasury/taxation/pdf/other_forms/tgi-ee/2009/091040i.pdf
You would deduct these contributions from your net profit on Schedule C and then enter that net amount on line 17 of form NJ-1040. Hence, the contributions will reduce your taxable income for NJ pension exclusion purposes.
See page 22 - http://www.state.nj.us/treasury/taxation/pdf/other_forms/tgi-ee/2009/091040i.pdf