Who should I get LOR from : manager of big prestigious company where I worked 5 years back, or unknown small company where I worked recently? I am applying for MS in CS. 6+ years of work experience.

I worked for a huge, globally well known company for less than a year straight out school. This was 5 years back.

I also worked for a very small unknown company for about 3 years. 

I can get letters from both, and the content of both will be about the same I think.

Which one should I use for applications? I already have 1 from my professor with whom I did research, and another from my last company where I worked. I just need to submit a 3rd one.
The badge, of whatever worth, for having worked in a "globally well-known" company is already in your cv. 

And, it is just "few months work straight out of school", begging the question "coffee anyone?" (only half-jokingly).

But chances are, in the "very small unknown company", your role was much more critical, compared. And it was for three whole years.

If I was the reader, it would be this second letter that would be more believable in my eyes if it mentioned anything about efficiency, professionalism, and dependability.