Master of engineering is a course for thus who want to further delve into engineering and its respective segments. Many manufacturing companies even sponsor some of their employees for taking up a masters' course in engineering.
MS or masters' in science is for those students who wish to participate and become a researcher in a given field. An MS degree promises to take a take a student deep into the subject to solve some of the most complex problems.
You should choose either one based on where you see yourself in the next five-ten years.