If my former boss is threatening me with fake fraud charges, what do I do?

If he believes you stole money in one way or another from the company, he can file a police report; if the authorities agree there is something there, you could potentially be charged or arrested--but if he does this and lies to do so, and it later comes out that he lied, not only would you be able to successfully defend yourself in court, but you could also sue him for filing a false police report and for malicious use of legal process (possibly also defamation). Therefore, if there is no evidence that you did take money, it is unlikely that he will or could do this successfully. He could also try to sue you civilly (e.g. file a lawsuit) for any money he claims you took, but again will need credible testimony and evidence: without proof, he will not succeed.
Separately, based on what you write (working at his office, under his direction), it appears that you were "misclassified" as an independent contractor (1099)--you appear to have been an employee (W2). As such, he should have paid the employer portion of social security and medicare taxes; should have provided whatever benefits employees received at his company; possibly you should have been paid overtime when working more than 40 hours per week; etc. You should contact the state department of labor to file a complaint for having been misclassified.