Depends on your interests and how much time you want to spend in one place. We did a road trip to the Maritimes around that time of year but had much less time than you do (we only had 13 days round trip out of the Toronto area, and first detoured down to Connecticut to visit friends before following the coast up.) While it is 'off the route' from Quebec to Nova Scotia I have included some things from PEI as well.
If you are looking for 'nature'-stuff, while you are driving through New Brunswick it's not too far out of the way to take a day and see the Hopewell Rocks (if you can be there for both high and low tide all the better). The Cabot Trail on Cape Breton is also great; in addition to breath-taking overlooks it also has lots of hiking trails of different difficulties. About halfway through the trail we also did a whale watching tour out of Bay St. Lawrence (they even allowed our puppy on board.)
If you are looking for adventure activities I can definitely recommend Deepelling with Open Sky Adventures in Fall River, New Brunswick just off the Trans Canada Highway. Tidal Bore rafting on the Shubenacadie River is one of those 'once in a lifetime' things-to-do (We were very happy, although exhausted, with the 4 hour 'extreme tide' tour from Tidal Bore rafting parks and cottages)
It would be impossible to list all the historical places to see, but touring Old Quebec City for a few days and a day at Louisbourg are tops on my list of 'military history' - and probably also the top of 'general' history.
For Acadian history Grand Pré should probably make the list and you might also consider PEI's North Cape Coastal Drive.
Cape Breton also lived up to it's advertising as "the Celtic Heart of North America"
As with historical places, there are far too many scenic places to list, but I think Lunenberg and Cavendish, the inspiration for Anne of Green Gables and also home to PEI National Park are on the 'must see' list - (Note: if you do plan to go to PEI I recommend scheduling it after Cape Breton and taking the Ferry out of Caribou, NS then driving the Confederation bridge from PEI back into New Brunswick).
A few other miscellaenous items: walking some of the famous stairs of Quebec City, or taking the Funiculaire de Vieux-Québec. I doubt St. Stephen, NB is anywhere close to your planned route (unless you are also dodging through Maine) but I'll mention the Ganong Chocolate Museum in case that interests you.
