The Resurrection Bay cruise does not get out of the bay - so you have calmer waters, but you miss a lot of the wildlife and the glacier viewing. I would suggest the 6 hour Kenai Fjords NP tour. I have taken it twice and it is excellent. If you are prone to seasickness though, I would take precautions. Both trips had people who were sick. The last trip was early in the season (May 2008) and we hit some rough seas. I would say half the boat was feeling it. Fortunately I did OK, even without medications.
The Kenai Fjords NP tour is fantastic -- definitely one of the real highlights of our 2 weeks in Alaska. That said -- it might get a little rough for a 5 year old. You'll have to be the judge of that. Resurrection bay will be a lot calmer, although you won't see as much.