Two lake boats in Fiordland and a short hop in Rakiura, none of them a timetabled ferry.
The Fiordland pair both start from lakes near Te Anau. The boat from Te Anau Downs to Glade Wharf is how trampers reach the start of the Milford Track, and it only runs in DOC's Great Walks season. On Lake Manapouri, a water taxi to West Arm goes when you book it, which is a different thing from the Doubtful Sound cruises that use the same lake.
Off Stewart Island, water taxis to Ulva Island leave from Golden Bay for the predator-free bird sanctuary. There is no printed timetable: you book a boat, check your bag for pests before landing, and plan to be off the island in the evening.