We pop over to Sydney quite often and have also joined/finished many cruises there.
Favourites.
Manly Ferry .
Leaves from Circular Quay, great trip, lunch at Manly, then back to town.
Bondi Explorer Bus ,
Leaves from Circular Quay. You can hop on and off as much as you like. Make sure you get off at Watsons Bay, view the Harbour Entrance, and visit Doyles Seafood Reataurant for lunch. Doyles is a bit "touristy" but its become an icon and well worth a visit.
Darling Harbour .
Great to wander around.
Opera House .
Do a tour.
Sydney is an exciting City.
Will 3 days be enough?