I would go for Waterloo, based on the following reasoning/assumptions.
Immediately post-graduation you will likely be working in North America and probably within Canada itself. Waterloo and the reputation of the maths department is going to be known in that local/regional context by employers.
When you come to take your MBA, whether you are applying to a North American or European school, universities will have heard of Waterloo and have some idea that it is repuatable, even if the general population hasn't heard of the place.
I am ruling out the possibility that you'd go straight to work overseas prior to your MBA for the simple reason that you'd probably not qualify for the work permit in the first place, regardless of which university you went to.
The work experience you get post-graduation will have a much larger effect on your chances of getting into a good b-school than the difference between Toronto and Waterloo. My personal opinion is that you should stretch yourself academically whilst you have the chance and are still in fulltime education. It sounds like Waterloo has the edge there.