We took the Mosquito Fleet whale watching a few weeks ago and had a wonderful time. The cruise was well thought out and respectful to the animals. It was a perfect full day adventure.
The ship leaves from the Everett dock very early in the morning (the only thing we didn't like!) and sets off for a three hour cruise to the area off the San Juans where the orcas usually are.
The Mosquito Fleet has a naturalist on board who explains a lot about the whales and the Puget Sound area. I liked how they handled the trip out because they made plenty of stops to point out wild life and told a little bit about the islands in the area.
The whale viewing was great. They gave us plenty of time to see the whales and didn't encroach on their environment.
After watching the whales, the boat stopped in Friday Harbor for a couple of hours so we could get lunch, stretch our legs and shop a bit.
Afterwards it was straight back pretty much at full speed, which was fine with us because the cruise time makes for a long day.
All in all we had a great time! If you're in Seattle/Everett and want to see the whales, this is the most convenient way to do it.