I live in Toronto and use VIA Rail to go to Ottawa and Montreal. If you fly to Toronto, take the UP train to Union and get a hotel downtown. You don't need a car in Toronto and can be kept busy downtown with museums, stores, and the lakefront. You can take a bus trip to Niagara - the drive is not pleasant. Buy tickets on VIA Rail Business Class in advance and go to Ottawa. It's very comfortable on the faster trains.You can walk or cab easily in Ottawa. Then take a train to Montreal. When you are ready to go on to Quebec, rent a car for the excursions you plan. Again, there's plenty to do without renting a car - excellent transit. There's good train service to Quebec as well and the city is compact if you stay downtown. A car will be a problem in most parts of the city. So, my advice is to take it easy and skip the driving. Of course, car rentals are available and there is parking - but it's very expensive. In all my trips to Ottawa and Montreal, I never had a car. When I've been in Quebec, I had a car because I was going to Gaspe, but I didn't need it at all in Quebec. And then you get your boat and are not exhausted. No dropoff fees and no problem.
Air Canada's flight are on Rouge, which is more crowded than their regular airline but it is nonstop and better than any US airline and UA miles can be used. All the others require changes. AA can get you here via Dallas, which is a reasonable hub. Avoid ORD. If you use UA, try for Denver.