It is relatively difficult to travel to and cruise other fiords than Milford and Doubtful Sounds.
However, there are a few operators that offer trips to Dusky and Breaksea Sounds, as well as to Preservation Inlet, and to more northern fiords.
In winter (May, August) there is a nice selection of tours available on the Milford Wanderer, operatred by RealJourneys:
You should also check out what is on offer with Fiordland Ecology Holidays. They have scheduled and charter cruises along the coast and into the fiords, including Dusky and Breaksea Sounds.
Also regular cruises around NZ lead around the fiords. However, those cruise ships stay outside the fiords, you would have to book extra trips into the fiords, if available.
I think cost-wise the winter cruises on the Milford Wanderer are the best option.
The trips start in Te Anau/Manapouri - nothing in the north, like Haast or Jacksons Bay.
For other tour operators and options, you best contact the tourist info in Te Anau:
A question that comes up in the Forum permanently is:
Milford or Doubtful Sound?
Here is a little write up:
I have been to Doubtful Sound once, and twice to Milford Sound. If you have not been to Milford Sound you have missed it all somehow. Already standing at the wharf, you get an unparalleled view.
Doubtful Sound is quieter and huuuuge and more monotonous, the bus drive between Lake Manapouri and the Sound is quite something. I really wanted to love Doubtful Sound more than Milford Sound due to its uniqueness and remoteness - but just could not. The snowcapped peaks at Milford Sound make the views much more dramatic. And already the drive to Milford Sound can only be described by one word: magic.
Plus: You can make so many side trips from the Milford Road at your own pace, short and long walks. You can stop at every lookout, the views are dramatic. On the Doubtful Sound bus trip I found the stop at Wilmot Pass with the view down to the fiord amazing, the rest was more or less through beech forest.
Every time we went to Milford Sound we went on an early cruise on a small boat, once with Red Boats, last time with Mitre Peak Cruises. 9am or 10am is good enough. We started at Te Anau at 7am and drove to M.S. at a leisurely pace, stopped many times, and went on the 10am cruise. There was not a single bus, just some cars. So it was not a touristy feel at all. When we came back from the cruise at around noon, the carpark was full of tour buses. But that was when we left. On the way back we made one 3 hour walk and several short ones. It added to the experience, and apart from the cruise with just a few fellow travellers we did not meet a lot of people, or just every now and then, whereas on a Doubtful Sound cruise you are always with a busload of other travellers.
We found the wildlife experiences at Milford Sound more interesting than at Doubtful Sound where you rarely heard a bird sing. Of course, this will vary from day to day, and the luck will turn.
A kayak tour might be different.
But again, if I have to choose just one of the two fiords, I would always choose Milford Sound.
And just a final word about the cost:
Cruises on Milford Sound are about NZ$ 70, more during the peak hours, as you can do the driving all by yourself, and the petrol for the return trip should not cost you more than NZ$ 20. For a Doubtful Sound day cruise you pay NZ$ 260 in summer and just about NZ$ 200 in winter.
If you can afford the time, do visit Te Anau's amazing Glowworm Caves, which is on the western side of Lake Te Anau. The few travel agencies in Te Anau all provide daily trips (once daily during off-peak and twice daily during peak) to the cave at prices of around NZ$45 each.
I recommend the evening trip for star gazers as the trip back from the glowworm caves during the night provides for unobstructed view of the stars from the top deck of the catamaran.
To summarise the experience of my visit to the glowworm caves in one word, I think "magical" would be it.
When I was looking up at the hundreds or thousands (or maybe even millions) of glowworms giving off their ethereal blue green light, it felt like I was in a tiny galaxy system. And not only that, the short trip to the glowworm grotto through the 15,000 years old cave system was also interesting, especially for city-dwellers like me.
The silence experienced within the cave was unreal, but also strangely comforting.
The culinary highlight for this region would be dining alfresco on the edge of Lake Te Anau - try fine New Zealand lamb or cervena (New Zealand venison), perfectly prepared with maybe a hint of Tuscany or an Asian influence.
The township of Te Anau offers a wide range of cafes and restaurants catering for all budgets. You can get everything from all day breakfasts and extra long lunches to gourmet dining worthy of the best clothes you've packed in your suitcase.
In Manapouri you'll find excellent cafe and restaurant dining with spectacular views of the lake and the famous Cathedral Mountains.
When you're perusing the local menus, keep an eye out for New Zealand salmon, rock lobster (crayfish), mussels, scallops, blue cod and perfectly tender local beef, lamb or cervena (New Zealand venison). International cravings are catered for with mouth watering Italian pasta and pizza and exquisite Chinese dishes.
Fine New Zealand wines, particularly from the Central Otago and Marlborough regions, are available at most restaurants. In some cases you can BYO (bring your own). Local wine shops carry a comprehensive range.