Beaches: Yes, there are beaches in the Alps! So if you (or, as is more likely, the kids) have had enough of traipsing around town, then you might consider retreating to one of the town’s two excellent, albeit grassy, beaches - one of which, on the western shore just south of the port, is shallower and therefore much better suited to families.
Lake cruises: On Lake Annecy, Compagnie des Bateaux run several boats daily from the quai Napoléon-III, including a one-hour trip, and a two-hour jolly which briefly stops off at various points around the lake.
Aquariums and zoos: The Aquarium du Lac d’Annecy may be small, but it’ll keep the young ones entertained for a good couple of hours.