Benoa Harbour, also called Pelabuhan Benoa, is a harbor and marina located to the south of Denpasar, Bali. It contains commercial as well as private boats. There is a good variety here, including a number of traditional vessals from different parts of the Indonesian archipelago.
There's plenty of boat tour operators at Benoa Harbour. You can chatter a boat from here for a day trip, or for a longer sojourn to far-off places such as Komodo Island.