I seem to remember that this is one of the numbered "Freedoms of the Air" that has to be negotiated between countries. Since the AC web site doesn't allow such connections, I would guess that there is no agreement between the US and Canada. Maybe there should be though. The railroads between the Northeast and Chicago had one route that passed through Canada and I think local traffic was allowed.
What I know is, if you want to fly from Toronto to Vancouver, you can transfer at
Chicago by NW. In the summer, this method is cheaper than AC but not the discount airlines. You may search exped??.com during summer, they will give
out such a result. The disadvantage is that you have to bring your passport,
that's all. I don't know the situation from US to US though.