A partial explanation might be that York is younger than University of Toronto and Western Ontario. Academic reputations especially for the "person on the street" can take a long time to develop.
International rankings have often viewed York as stronger than Western and having a similar rank to that of Toronto (as always, I urge readers not to take these rankings too seriously).
For instance, EIU 2004 ranked York far ahead of Western (#22 vs. #75!).
FT2005 again places York ahead of Western (#22 vs. #34) and just behind Toronto. FT2004 again placed York ahead of Western (#22 vs. #29) and near Toronto.
A look at CEO production might be informative as well. Note how two major financial services firms in Canada are headed by York MBAs (Scotiabank and CIBC).
The following thread covers some Canada MBA issues:
https://www.gmatclub.com/phpbb/viewtopic.php?t=17007