I was discussing my proposed trip last weekend with a family friend of about Margo's vintage. One of the friend's brothers was either about to take or was thinking about taking a motorcycle trip that resembled my proposed trip as he was going to Newfoundland from central Quebec. However, he was planning to ride along the North Shore of the St-Lawrence until the road runs out. From there, he was going to take a ferry to Newfoundland.
I must admit I had given it a brief bit of thought, but the logistics of it don't work for me. This northern route has more hills and fewer towns. Too few towns for my liking. It is one thing if you are on a motorcycle to push on for 50 km to reach the next down, but quite another on a bicycle. In addition, I believe the ferry service in question is far less frequent than the North Sydney to Port-aux-Basques run. If memory serves from my initial investigations, the latter service is something like twice a day in high season. I would be surprised if the former was more than once a week. I would spend too much time worrying about timing my arrival to match the ferry.
I found the website of the ferry company that serves the Lower North Shore, Relais Nordik. This took some doing, namely looking up the Harrington Harbour website. It was the first village in the area I could think of owing to the fact it was where La grande séduction was shot. There is in fact 1 ferry a week, taking 3 nights to get from Sept-Îles to Blanc-Sablon. Not terribly useful. It also asks that you book your vehicle at least 30 days ahead of sailing and ideally 180 days! I am not sure if this applies to bikes, though it likely doesn't. ;-)
One off-beat option that the Relais Nordik website brings forwards is the possibility to sailing from Rimouski on the South Shore to Sept-Îles and from there to Blanc-Sablon. This could cut about two weeks worth of cycling, but I wouldn't get to see New Brunswick or Nova Scotia. However, it would add the best part of a week on the ferry. Chances are I would go stir-crazy on the ship.