There is a joke that goes something like, 'you can't have a best Canadian film as it is an oxymoron'.
Only self-loathing Canadians (some Canadians are) say things like that. For the sake of streamlining my argument, I am going to count English-speaking cinema only. Besides, it ain't fair; on average, Quebec movies are way ahead of their Anglo cousins -- so my first pick would be Don Shebib's 1969 super flick, Goin' Down the Road.
Hold on a moment: Goin' Down the Road is not the best Canadian movie ever made. The best Canadian movie ever made is Starship Invasions.