I think it is likely that you will see whales from the cruise ship. If you want a closer look, Orca Enterprises out of Juneau has received many good reviews. We are going to go with them while in Juneau. Their web site is www.alaskawhalewatching.com. You have to reserve directly with them, not through the cruise ship.
It is possible to see whales from the ship. Will you see them all depends on if you are watching at the right time. Keep watching for the blow from the whales when near a window or out on deck. The blow from a humpback can go 30 to 40 feet in the air so it can be seen and heard from quite a ways away. Watch for water disturbance that may be whales coming up to feed in a bubble net. Breaching is more common in Hawaii but does happen in Alaska. You will see more tail roll than breaching. The ships always tell you that Orca are active between Victoria and the inside passage but I have never seen them there yet. I see them in Juneau and Seward or in the fjords near the glaciers.
If you want a whale watch Capt Larry in Juneau is excellent many naturalists from the ships use him.
Also keep your eyes open for porpoise you can see them frequently.
Have an old friend who just posted on another site that she saw so many whales this time it was awsome and it was with Capt Larry-- we were there last year at the end of June------
Another friend-- said the same thing but dont know if she saw them from the ship or on a tour
Enjoy and cheers
I just returned yesterday morning from a two-week cruise in Alaska.
On May 24 in Juneau with Orca Enterprises (Capt Larry) I saw about five different humpbacks. Two of the five gave us a 'tail flip'.
On May 26 in Sitka Bay I saw about five Orcas right off the port side of our ship as we cruised away from the beautiful port of Sitka. They were very close to the ship, and the only Orcas that were spotted during the two weeks I was on board the Carnival Spirit.
On Jun 1 I saw one humpback from the ship as we cruised into Skagway around 06:00. I watched that one whale for about 1/2 hour as we approached the harbor.
While I have seen more whales on a previous cruise in Sep 2000, I feel very fortunate with the sightings during the past two weeks. And, lots of sea otters were cruising College Fjords on May 29 with their pups.
I also just returned from an Alaska cruise (Coral Princess) and saw a few humpbacks from the ship. However to see them up close, take a whale watch tour out of Juneau. I'd read great reviews of Captain Larry as recommended above. However, since there were 6 of us we opted to book with Juneau Sport Charters, Bob Mothershead so we would have the boat to ourselves. The boat was the Dreamcatcher, a 28 foot Bayliner, and was $350 for a 4 hour trip. For another $25, he will pick the group up whereever you are and return you to town or the ship. On the way back to the ship, he stopped awhile at the Mendenhall glacier. In addition to seeing a number of humpbacks up close, we stopped on the way in for a great display of eagles feeding.