Yes, your boss has the right to fire you. In the private sector, employment in every state but Montana (and even including Montana in some cases) is considered to be at-will. That means you can quit at any time and for any reason, and you can be fired at any time and for any reason that does not specifically violate the law. The question here, is whether ot not your boss's reason violates the law.
Given the information you have provided, no, you were not wrongfully terminated. I'll explain why:
Your boss is required, under the law, to pay you the full amount due you. However, nothing in GA law offers you protection if you make an internal complaint. If you had gone to the GA DOL and complained about the short checks, and then you had been fired for that, that would have been a wrongful term, because the law does offer you protection if you complain about illegal activity (not paying you in full) to the appropriate regulatory agency. But you don't have protection for, in effect, going over your boss's head to complain.
I want you to understand that I am not defending your boss. It was morally and ethically wrong to fire you for complaining about the short checks, even if it was not illegal. But nothing you describe gives you LEGAL recourse.
While you have no recourse for the firing, you do have recourse for the short checks. It is not entirely clear if you actually are an independent contractor, or if you are an employee being treated as an IC. If you actually are an IC, there is nothing in the world stopping you for suing him in small claims court for the amount still due you. If you are an employee, then you would need to file a wage claim with the GA DOL.