I worked for a medical office and my salary as manager was suppose to be $48,000 yearly. I have been shorted several pay checks as there was not enough money to pay me. I am no longer working there and recently received my 1099 for the year and it showed that I was paid $17,000 for NINE months, I should have received over $30,000 by September (those NINE months). He refuses to pay me. Please advise what rights I have and what legal recourse I have from here? Thank you!

First if you were paid as a 1099 worker, you were not an employee but a independent contractor which means he was not withholding or paying taxes on your income, ( which is going to have to be paid as such when you file your taxes ( assuming you are in the US)

Next you know as a 1099 you were not covered by unemployment insurance and not covered by workers comp.

At this point you have to sue them in court.