First off, congrats on your anniversary and your first cruise to Alaska. I've done Alaska 10 times, and July 9 will be my 11th time as I'm doing the Grand out of San Francisco with my sisters.
I've done whale watching in Juneau a couple times, once thru the cruise line (Princess) and once with Orca Entrerprises (Capt Larry) in Juneau. While I enjoyed both, Captain Larry was outstanding, they know the times the ships arrive etc and work with you. They use sonar to find the whales.
In Skagway I love the White Pass / Yukon combination.
Ketchikan, I just love to stroll around the town.