The three tours that you have mentioned all come highly recommended from what I have read on the message boards. You might check out www.cruisecritic.com - there have been a lot of comments and helpful advice that I have read there. Hope that helps. Happy sailing.
We have done whale watching in Juneau several times with Captain Larry at Orca enterprises. We are booked agian for September I know several others have used the same company and been very happy with them. www.alaskawhalewatching.com
In Ketchikan we were recommended to use Island Wings for a flight over the Misty Fjords . It is owned by a husband and wife.
We couldn't fly with them as the weather was very bad and they said it would be a rough ride and the view not very good due to the heavy rains. We received a full refund.
We have booked with them for this year. www.islandwings.com