Le Commensal is a popular vegetarian restaurant in both Montréal and Québec City (in Québec City, it's a few blocks outside the walls of Upper Town at 860 rue St-Jean). Aux Vivres is a popular vegan spot in Montréal's Mile End.
Two websites in particular, HappyCow's Vegetarian Guide (www.happycow.net) and VegDining.com, list other vegetarian options in Montréal and Québec City.