I agree with highhopes. Schools exercise discretion in the admissions process and as long as your recommender doesn't tell anyone, your supervisor is unlikely to find out (at least until the background verification stage). Unless you're admitted, you're not entered into any sort of database that alumni have access to.
Regarding your choice of recommender, I would pick someone who: 1) thinks highly of you and 2) can demonstrate that they have sufficient understanding of your skills and work ethic by providing specific examples. This person does not have to be your direct supervisor. You can ask someone at your work who has supervised you perhaps on a few projects, or even a client.
Depending on your recommender selection and the school you apply to, you might have to explain this briefly in the optional essay, but this is nothing you should worry about. Plenty of candidates do not approach their direct supervisor every year, so your case would not stick out. As long as you have a good reason (and I would strongly advise against volunteering info such as that your boss doesn't think highly of you), no adcom is going to question said recommendation. Job security is perhaps a good reason and one that many candidates use. As an aside, feel free to provide your recommender with a bullet point list of areas you'd like them to touch on in the rec, but do find a recommender who thinks enough of you to write your recommendation for you and not ask you to do it yourself.