Okay guys, now I'm really confused. I emailed the NZ government customer service and got this response:
"Hi Dawn,
Thank you for contacting us.
To answer your question, yes you will go through the customs at Port Chalmers in New Zealand.
It is also recommended to declare the medicines even if you are going to leave them in the cruise ship as they will be a part of your luggage."
They make it sound like we'll be dragging our luggage off the ship to go through customs at Port Chalmers!