There is never going to be a Toronto water commuter service except to the Toronto Islands.
Ferries work best when they cut directly across bodies of water (like the Dartmouth Ferry or the Vancouver SeaBus), or when they serve locations that are inconvenient by surface transport. (Like connecting mainland Vancouver to Granville Island.)
In Toronto, none of that materializes at a scale suitable to support a commuter service: instead of cutting directly across a body of water, ferries would have to run laterally along the coastline, often directly parallel to much more efficient methods of surface transportation.
Certainly, there will be summertime demand for touristic trips between Ontario Place and Harbourfront, or whatever, but that's not a commuter service. You're never going to see a SeaBus system, at least not without a level of subsidy that would make your eyes pop out of your head.
Even a service between Ookwemin Minising and downtown... for one thing, it doesn't go downtown: you still need to transfer onward to reach the downtown employment area. And once the Waterfront East LRT comes online, offering a direct trip to downtown in a single seat, demand for a commuter ferry along the route will evaporate.