It depend on what you want to do on the harbour cruise - do you just want to spend time on the water? Or sightsee? Or cruise and have lunch or dinner? If sightseeing, I would suggest you catch one of the harbour ferries and visit Manly where you can walk through to the ocean beach, have a meal at one of the many restaurants or eat fish and chips sitting on the beach. Perhaps take a walk into the Sydney Harbour National Park. Another suggestion is to catch a ferry to Parramatta, a historic suburb, which will take you under the Harbour bridge and up the Parramatta River. Or a ferry to Watson's Bay which on the other side of the heads to Manly.
If you want to do a harbour cruise just to spend time on the harbour, as you said there are plenty of options.