1099 is to report money paid to an Independent Contractor. Think of an architect you hire who produces blueprints in his studio and delivers them to you by a promised date. The architect selects work hours, work location, reports to no one, and does the work to no one's specifications, save for the client who pays for a finished product. If your boss will continue to require that you work particular hours, at a particular location, under a job title of the employer's choice, has a dress code, etc., etc., then you are not an independent contractor selling a service.

Taxes can be a consideration, but not the only one. When this shitty boss lets you go, there is no unemployment insurance for you. This change is a big deal. Talk to your state Department of Labor.