Sitka is hit or miss for whale watching. (As mentioned recently in another thread, Sitka doesn't have any glaciers either!)
The Taku Glacier Lodge is a great tour. I go about every 2 years now that it's owned and operated by Wings of Alaska - used to be a family business, now it's not.
There are many great whale watching tours in Juneau. If you don't have time, Icy Strait Point (Hoonah) is the other port best known for humpback viewing.
The other option would be to take a tour to Tracy Arm or Taku Harbor... there are several good charters in Juneau that will prepare a wonderful lunch, find whales, show you the icebergs and glaciers... basically everything BUT the flight.
Better not for now... signatures get me banned!