How to decide which recommender to ask for LOR? I have found a few similar questions on this issue, but none that have solved my dilemma.

I am currently applying to PhD programs (US, natural sciences). I need three letters of recommendation for most programs. I have already decided to ask an advisor I spent a summer doing research with, and my current research advisor (I've only completed the research proposal so far, but I've had several classes with her as well and she knows me well.)

For my final recommendation, I'm trying to decide whether to ask my academic advisor or my supervisor from my industry job.
I've had many classes with my advisor, and discussed my plans to go to grad school with him. I think he would write me a very positive letter, but would probably say things that are similar to what my current research advisor would say. 

I've worked at my current job which is related to the field I'm going into for only about 5 months now (3.5 months full time, the rest part time). In that time though, I've gone above the duties expected for interns because I am a fast learner. I also worked overtime almost every week while I was working full-time, was asked to give a presentation to the whole company at a monthly meeting (usually only supervisors give these presentations), and have helped to train new employees. I feel that I would get a very positive LOR, but I worry that admissions committees will not be interested because my recommender only has a BS degree and my job is not research-based.
Go with the supervisor from your job.  The schools will have your transcript.  Unless there's something special the adviser can write, this is a no brainer from my point of view.

An example of a case where there is something special the academic adviser could offer would be if you have any warts in your transcript that you think your academic adviser can help you explain by way of the letter