http://www.baseball.ca/eng_doc.cfm?DocID=72
There's a list of a lot of Canadian players. Anybody from Brampton, Mississauga, North York or Richmond Hill is basically from Toronto in my opinion because those other cities weren't included in the game but they're close enough to the GTA. Heck, North York is part of Toronto. This goes for Shawn Hill, Russ Martin and Pete orr.
Scott Thorman, born in Cambridge, I tend to use Kitchener for him because his high school was pretty much right on the border between the two cities and Cambridge isn't in the game.
Erik Bedard, I use Ottawa because that's about the closest place I can find to Navan.
Justin Morneau is from New Westminster, but the closest city to that that's actually in the game is Vancouver. Pete LaForest is from Hull, QC but I generally tend to just use Ottawa or any other Quebec city for him. Ottawa is close enough.
Anybody else, I'd just go with the cities in their names. Toronto, Vancouver, Victoria, Kitchener, Sechelt, Montreal...they're all in the game.