We did the inner passage cruise a few years ago and everyone loved it (us, 3 kids who were 3.5, 7, and 9 at the time, 2 sets of Grandparents). We did one room for the 5 of us at that time but one of our boys would go to the grandparents for the night most nights. We just weren't in the room much and the Disney room with 5 beds was OK, but I wouldn't do it again. We did get 2 rooms on our other cruise with the kids. For 3 of you, one room should be fine.
I would love to go to Anchorage and Denali sometime, so if you did the cruise along with that, which I know exists, that would probably be awesome.
Mama to my boys (04,07,11)