If you really want to see Penguins, skip those at Simon's Town completely. Rent a car and head to Betty's Bay. It's a two-hour drive from Cape Town, and the section along the coast is very pretty. There must be 5-10 times the number of Penguins as Simon's Town, and 1/10th the number of tourists. Maybe even less. No long lines... no lines at all in fact. The photo below is only a small part of the colony.

Penguins at Betty's Bay, South Africa