There is another way:
You go on the ships owned by the State of Alaska...The Alaska Marine Highway.
They are more genuine. They have decent cafeteria food, clean rooms, Forest Service Guides. The cost is less. You book in early January. We have done it twice.
Start from Bellingham, WA. ( They have an airport, or you can shuttle from SeaTac. )
Here is the idea... You want to see the route up thru the Canadian Gulfs, the Dodd Narrows, the 300 miles of Vancouver Island and its camps. The whales. Then crossing the Queen Charlotte Straight. Then the Inside Passage coming to Ketchikan, Wrangel, Petersburg, then Juneau. You can go up to Skagway. We always like going to Sitka.
The cruise ships dump you in these towns with a crowd to buy trinkets, then they travel mostly at night, so you miss Southeast Alaska. The Ferry goes any hour of its schedule. They must have 5 or more ships.
But it is how you do it that makes it fun: You ride to say, Ketchikan. Get off to a local B&B/Hotel. All on foot. Stay a day and enjoy the town. Catch another boat going North. Try and stay in Petersburg as it is a European-Settler -Based fishing village. ( Eat Halibut!)
Then North to Juneau. Great museum and glacier. Tram Ride, helicopter ride to glacier...it is 100 miles long.
Decide: north or west or both, but Sitka is a must. It has the now State run Sheldon Jackson Museum of the Tlinket Culture including many Totem Poles.
You can fly back to Seattle or take the boat. The best time to reserve is when they release the schedule in January. You book ship...book B&B, book ship, boat B&B. May thru August is best.
Much less focus on booze and casinos. You see a lot more. The big cruise boats can not get to Petersburg.
We also did this once on an old classic Holland America ship, and the best was when I purchased Nomad, a 40 foot trawler in Juneau and drove it home to Orcas Island, WA
(photo in my edit: )
Want a heart warming book about a family, eventually a widow lady raising her kids on their fishing boat near Petersburg? This is a good read to understand the Southeast culture. Take it along!
[ame]https://www.amazon.com/Following-Alaskan-Marilyn-Jordan-George/dp/0967163919[/ame]