Do you want to cruise from Australia or from a NZ port? Most mainstream cruise lines do a round trip from Australia to NZ and back - sailing from Sydney, Melbourne or possibly Brisbane. There may be a small number of one way cruises from Australia or NZ (Auckland).
My favourite destination is Fiordland for NZ, then Dunedin, Tauranga and Auckland. From Tauranga, you can visit the Hobbit movie set and film locations or visit Rotorua for the hot springs and Maori culture.
Fiordland - the ship usually sails into the sounds for the passengers to have a good view of the scenery. Depending on the cruise line, you may visit 4- 5 sounds including Milford Sound which is the best (I think). In Milford, the ship will sail up the sound almost to the end where the village is situated and turn around to sail out. If there is an overnight excursion from the ship, depending if the ship is sailing from or to NZ, the ship will stop while turning for the excursion passengers to either disembark or embark. A point to remember is that depending on the weather conditions, ships may not always make it into the sounds.
I would suggest you do some research on the NZ ports and what their attractions are. That way you will find which ports will suit you most and you can choose your cruise accordingly.