The cruise highlight is the sea caves. There is also narration much of the time about the Apostle Islands. Unless you just want to be out on the water though, I would suggest that you skip the $40 cruise that is 3 1/4 hours and instead go to the little town of Cornucopia. I have not done this but there is a hike of 1.8 miles which takes you to some sea caves. I am sure this is better than the cruise.
If you do the cruise, have to go early to get an upstairs seat for the best view. If upstairs, however, you will be subjected to the wind and sun and need to be prepared. To see the caves even better than on the hike, if you kayak, go by kayak. There is an excellent outfit when approaching Red Cliff that takes groups by kayak.