Is it okay to get a letter of recommendation from my employer who is a scientist but not an Ph,D?
When reading a letter, the specific academic qualifications of the writer are not that important, judging their knowledge is. You say he works in research, so presumably he can gauge your technical skills (unlike, say, some administrator that just handles your payroll).
Furthermore, if your boss has enough experience supervising people, he can give a better assessment than someone who only has had one student.

In any case, you already have two letters from experienced professors. A third from a more junior person that has worked closely with you is still valuable, and not everybody has worked with three different professors. So you are fine from two different perspectives. It is up to the reader if they want to ask for them, or read them, or not. My girlfriend, for example, gave both her supervisor and a postdoc for an industry research job, but they only asked the professor and she got hired.



One caveat: the recommendation letter culture in academia and industry is very different. Make sure your boss is aware of that. A letter saying:


  Eren has worked in my group in COMPANY with the title POSITION between 2015 and 2018.


may be what is expected in industry, but it is a field of red flags in academia because he doesn't have anything nice to say about you.