The Musée naval de Québec is a small maritime museum near the old port, focused on the naval history of Quebec and the St. Lawrence. Objects, photographs, models, and temporary exhibitions give it more depth than a quick harbor display.
It works best as part of a lower-town walk, especially if you are already visiting the market, the old port, or the Musée de la civilisation. Allow less time than you would for the city's major museums.