When considering which program to choose, always consider where you are heading in the future. This is the most important factor when comparing these two programs. Both degrees will serve you well, and whether one is better than the other depends solely on your career goals and how you plan to utilize your degree. Typically, an MBA program offers a more general education than an MS. However, MBA programs are constantly evolving, and they now tend to put more stress upon specializations and concentrations.
Another thing to consider is that MS programs are not subject to rankings like MBA programs are. Therefore, the prestige that is carried with MS programs is much less discriminating.
Academically, both programs are usually similar in difficulty. There are some that say students in MS classes tend to be more academically inclined because they are there for different reasons than MBA students. This opinion is based on the thought that people who are going for an MBA are in it for the money, the career, and the title. Where as MS students are in it for other reasons-- most of them academic in nature.
Because not all schools offer an MBA and not all schools offer an MS in business, your first decision will be to decide which is more important, your program of choice or your school of choice. If you're lucky, you can have it both ways.