Was told a while back that the only reason there is a YYZ base to begin with is because the flights used to go through ANC and rosters were easy to handle. When direct flights were started, they didn't want to close the base so they continued.
There was no JFK base before and they want to keep it that way because of the direct flights. Although there is the JFK-YVR sector, the YVR base is over-crewed with Captains and hence that short sector is already fully given to them. No room to send potential JFK based guys on that short sector as well.