There are 2 day trip boat cruise operators on Doubtful Sound;
1. Doubtful Sound Cruise.com http://www.doubtfulsoundcruise.com/ offer a smaller day trip limited to 40 people
2. Real Journeys take around 110 people.
Of couse these are the maximum numbers and they may not be full on the day.
Alternatively you could do a kayak and boat day cruise with Adventure Kayak and Cruise http://www.fiordlandadventure.co.nz/, they are limited to 2 groups of 8 people maximum.
If you have the time and money I would recommend you do an overnight cruise on Doubtful Sound, the fiord is so big that to really appreciate it I would recommend spending as long as possible on it (and you get the advantage of getting weather changes during this time). For a search of all operators go to the local Fiordland site www.fiordland.org.nz. The overnight operators all offer smaller groups of around 15 people (except Real Journeys).
All the trips depart from Manapouri or Te Anau so you will need to travel to this point. This means either getting a hire car, or Tracknet www.tracknet.net have a regular service between Queenstown and Te Anau. To keep things really simple you could just travel with Real Journeys, they have a bus departing Queenstown for their overnight cruise at 9.30 am daily... but the down side it is the biggest operator, catering for 70 people on the overnight cruise.
Good luck with your travel planning!