Officially, you'd be on your own to buy a new ticket to NYC. However, you should at least find your way to an AC connections / customer service desk for your missed 'connection' due to late AC int'l flight. I've overheard them help people who missed a flight for dumb reasons or even a competitor's inbound delay. I've also heard them deny any rebooking assistance to someone who took an extra hour for additional security screening.

Also, keep in mind that AC NYC flights seem delayed far more than Tokyo flights. You may find yourself with enough, or even extra, time in YYZ.