Real Journeys do a day tour from across Lake Manapouri, through the underground power station and then across to Doubtful Sound. the details can be found here on their website, www.realjourneys.co.nz
Suffice it to say that while not the cheapest it was very well organised and an absolute pleasure to go on. A full day, pick up at the hotel at 7:30 thank you very much, but better than the later one in our opinion.
It would be hard to pick a highlight as it was all so good. It was raining of course, but rain forests tend to be like that.
Sadly dinner at the Keplar was nothing like La Dolce Vita cafe. I guess the warning was loud (free glass of wine when you present this card, the girl didn't know where the 'fresh' fish came from and worst of all battered local fish with chips, salad and two eggs. Oh dear. OTOH Mary's scallops were good so you take your chances.)
We just made it back to the motel before the rain started so that was lucky.