Which do you think would be more lucrative in the long run? I am in computer engineering, and I would like to do my own startup, but I am exploring other options as well.
It's hard to really make a call on a questions as broad as that. There are a lot of MBA programs out there. I'm sure some are pretty good, others not so much. I have no idea what "natural science management" is.
On top of that, with any business-oriented education, the program itself will only count for so much with respect to how "lucrative" it is. What matters is what you do with it.