I worked for a company that was trying to set up a seaplane base for sightseeing in Toronto harbour in 2000. All I can say is the idea was looked upon extremely unfavourably by the Toronto Port Authority. A bit of help from the mayor's office (but that person is no longer there) but still no joy. Witness the YTZ bridge/election debacle of 2003 and the protests that were raised by the island residents and you have a small idea as to the hurdles such a service would face.
The current mayor, the port authority, and the island residents would all vigorously oppose such an idea regardless as to the economic benefit it would bring to the city and waterfront. Really too bad as there is such a service off the east river in Manhattan (which Toronto loves to fancy itself akin to), Sydney, Seattle, and of course Vancouver and the entire west coast of Canada.