You could just put the Toronto HSR station in Hamilton and connect from there to the Toronto metro system assuming it has one. That saves you the "jog". Also I think that the second time you mention Lake Ontario you mean to mention Lake Erie which is the real NY-Detroit obstacle, which is what motivates going through Canada.
Reaching the absolute minimum NY-Chicago travel time isn't necessarily the highest priority because at that distance you're not going to beat a plane and you're probably not going to see same day round trips. Instead making the line economical by including as many people as possible would make the trip cheaper for people who can't afford flying. You could even add stops in Philadelphia and Toledo, which aren't too far off course.
Reaching the absolute minimum NY-Chicago travel time isn't necessarily the highest priority because at that distance you're not going to beat a plane and you're probably not going to see same day round trips. Instead making the line economical by including as many people as possible would make the trip cheaper for people who can't afford flying. You could even add stops in Philadelphia and Toledo, which aren't too far off course.