Here are a bunch of operators who work in the region worth checking out. They're adventure travel companies, so generally operate smaller cruises.
http://www.adventure.travel/searchpage.aspx?category_ID=273%2C276%2C62&page=1 over 6 years ago
Take a sleeping bag and ride the Alaska Marine Highway Ferry. If I'm not mistaken you can get a pass for it so you can hop on and off as much as you like during a particular timeframe.
It is very common for people to sleep wherever there is room. Many people bring a tent and sleep up on deck.
During the summer months there is a National Park ranger that rides the ship and gives lectures and wildlife spotting for passengers.
It really is the way to see Alaska since you can get on and off stay at little B&Bs in the villages, the ferry takes the exact same route of a cruise ship, and is is 1/4 the price of a cruise. over 6 years ago