Ucalgary I've heard is good.
Hm. From what I understand, there is only one SM course offered in their BA program, and it's an introductory one. I wouldn't put U of C near the top of my list.
I would definitely apply to NTS (very competitive, but worth it just for the application process). U of Alberta in Edmonton offers (I believe, correct me if I'm wrong) the only specialized BFA Stage Management program in the country. I may end up applying there sometime in the future, I haven't quite settled on it yet. There's a lot of opportunity within the program, and I believe you are able to earn equity credits before you graduate.
From what I understand, UBC, Studio 58, York and Dalhousie are good programs.
I went to MRU in Calgary. It's an intense conservatory style program. I liked it.