September is beautiful in Quebec, the leaves on the Maple trees are all changing colour and it's not usually cold yet. Quebec City is a beautiful city (not much to do in Beaupre though). Drive into the city and spend time walking through the old walled city, take a short river cruise, eat on Grand Allée (street lined with restaurants all with sidewalk patio seating).
Montreal is pretty nice too, it's a big metropolis that has a some charm, Quebec city is much smaller and much more charming. But I think September is a great time to go. Quite a few of the cruise lines offer cruises to the St. Lawrence river from Boston and New York in the fall because it's so beautiful with the leaves changing colour and the comforttable temperature.