How you file depends on whether or not you are an employee of the company you work for.  How he obtains a contract is not relevant.  

If you are an employee of the contractor, meaning he pays you and deducts all your social security and federal income taxes from your paycheck, then you would receive a W-2 from him and would file as an employee.

If he pays you gross wages and does not withhold tax for you, then he would give you a 1099-Miscellaneous form to report your wages and you would file as self-employed.

Talk to the person you work for and find out which form you will receive.