Consider taking the Espanola-Manitoulin Island-Tobermory route as suggested above, as Southern Ontario has more parallel routes on quiet county roads compared to the rugged hilly north. Sudbury to the Ottawa Valley (into Petawawa) can be quite a challenge as the highway is narrow and steep at times with no alternative routes. Having said that, I've cycled across that expanse twice and I'm still in one piece
I rode through the south of Lake Superior last year and the roads in the UP are a mixed bag. Some stretches have no shoulder but traffic is generally light.
If you decide to ride along the shores of Lake Ontario and the St-Lawrence Valley, that route is documented here: http://www.waterfronttrail.org
As already mentioned, the Route verte in Quebec makes getting around by bike in that province really easy.