Comparing between MBA and MS is literally bringing the apples and oranges argument all over again. MS is tailor-made for science and engineering graduates who wish delve deeper into their field of graduation to become a true specialist of their field. MBA is for students who wish to turn their career in a different direction to take on a major hands-on approach in areas of management and finance.
Between these two, the choice is purely subjective and up to you. None of them is better or worse. They are what they are.