I would need to know a lot more about this, but my first impression is that you have a state claim and a federal claim. The federal claim would not be adjudicated in state court. It may be possible to have one case, but it might need to be removed to Federal Court (the whole case including state and federal claims).
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Understand that there may in fact be three claims: (a) employment claim, (b) failure to pay and remit taxes to the IRS or pay the correct Federal Income Tax, and (c) the same as (b), but the failure to pay NJ taxes, which can be joined with your NJ Law Division claim.
Be careful that the tax/whistle-blower claims are not being used for leverage to win your employment case for if threat of such claims is made it could backfire and result in you being accused of extortion.
Any such claim asserted is supposed to be referred by the sitting judge to the proper tax agency. If you advise the Division of Taxation, and the IRS directly, you can win, if valid claims, a percentage of the amount recovered. I think this is a better approach assuming it will not cause the former employer to go bankrupt and make your employment claim worthless.
While the whistle-blower claims be brought, the reality is that the trial court has no ability to do anything other than to refer it to the proper taxing agencies.
The foregoing is not intended to be legal advice upon which you may rely as I have not been retained for this purpose.