I believe you see the whales from the ship on most sailing, but it's a much different experience to go on a whale watching tour, in my opinion. From the ship, you're very high up, even if you're just on your balcony, and it's a very different perspective to be in a small boat down on the water with a close view of the awesome beauty of the whales. The one advantage of viewing from the cruise ship is that you can see a lot further than in the small boats, but then you can't go closer to the whales. It's just exhilirating (sp??) to see from the small boats. We went in a Kodiak raft to orca watch from Victoria (precruise while staying in Vancourver) and saw orcas and humpbacks on an excursion to the Kenai Fjords park out of Seward, and I can highly recommend both of those trips. There are so many things to do in Alaska that it's difficult to narrow down, but I think we would have missed a lot if we had left the whale watching off our list.
Yes excursions are necessary- if you have the interest to see whales. It requires a GREAT deal of time invested at the front of a ship, properly dressed with a good pair of wide angle binoculars. Very very few passengers are willing to do this. You need to know the likely areas and be willing to accept a minute of distant views for all the time needed. You are always a great distance away and the ship never stops. Out of Juneau - you are likely to see humpbacks- close to 100% sightings, orcas only come in an average of 5-10 days. Out of Seward- you need at least 6 hours on the water. This is route trip with the feature- VARIED wildlife, whale sightings can be none but never extensive viewing as in the specific whale watching tours. Friday Harbor Wa and Victoria Wa. have orca tours. I greatly prefer the zodiac trips, but reserve ahead as they take fewer people than the regular boats. I have done them all.