"That's what I've understood but will refrain from passing this on to our friends.
Without hijacking Aaron's thread I'd like to know what a better way to see Alaska may be? No motorcycles Jim, those days are past for us.
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I would fly and then rent a vehicle. Or fly in and rent a smaller boat. Or a combo of both. There is a decent highway system, but there are quite a few landlocked cities where there only access is by air, sea, or birth canal. The State Ferry system is well run though and offers a lot of access.
You still have access to all the same companies, more actually, that the cruise lines use for their daily excursions. So I would do my research and order planned day trips personally. Probably work out to be cheaper in the long run as well as you planned in advance. And the locals are so thankful that you are willing to spend your hard earned money with them and not the Cruise lines that they will treat you like a king.
I and a friend have been planning a back country Alaskan trip for a couple years now. We will be going the motorcycle route, and planning all our own activities. Looking like it will cost about the same for each of us to stay and play for 2 weeks as the 8 day cruise and all the extras my wife and I did.
Anyway you decide to travel, you will be happy you did. It is an amazing land, and I honestly yearn to go back already.