Most people would say the best route is highway 138 on the north shore, which happens to be the Route Verte #5. It's a major highway with shoulders but relitively quiet since the parallel highway 40 takes up most of the traffic. IMO, the best part is between Trois-Rivières and Donnaconna. I like to ride on the south shore from Montreal up to Sorel (ferry) but there's a 12-15km stretch that really sucks on highway 132 because of high traffic, lack of shoulder and really bad pavement. Maybe they fixed it.
If you have time, you could ride a little more inland, something like this very rough route: http://maps.google.ca/maps?saddr=Mon...b&z=8&lci=bike
I biked most of it and it's quite nice. Some is actually another Route Verte (#8?). From Rivière-à-Pierre to Quebec City, it's bike trail from nature to downtown Quebec City.
A completly different route would be inland on the south shore, almost all on bike trails, mostly rail-trails, usually on Route Verte #1. It does get a little boring except around the Eastern Township section. It looks a bit like this
but Google Maps is missing many many trails. For exemple, between Richmond and Levis, it's one very straight rail-trail.