We tend to shy away from crowds, so we knew the crowded Milford cruise boats were not for us (the smallest takes about 80 people). For $115 each, we got a private kayaking/hiking tour with Rosco's that included a few hours on the Milford Track. It was just the two of us (in a double kayak) and our friendly guide, Emily, a native Kiwi. She was very knowledgable about the area and quite fun to talk to.
Rosco's offers several tours of the area, but none that pair more than 8 guests with a single tour guide. They launch from the fishing docks, so you won't have to grapple with all the tourists loading on to the giant cruise boats. The trip is very serene and quiet. If we had had more time, I would have loved to do the 5-hour kayaking trip to the Tasman Sea.
The views of Milford Sound are incredible. We were worried because it had rained the night before, but that only added to the beauty because the waterfalls were swollen with water. You won't believe how many you can see after a rain. By afternoon, the skies had completely cleared, and the sun was shining.