Here is a site that might help you http://cruiseportinsider.com/index.html
Also the Pearl arrives in Juneau around 1:45 PM and leaves around 9:30PM - in Sept it will be getting dark - even in late June it was what I consider dusk when we arrived back from our tour around 9:00. The attached photo of the Pearl was taken from our tour boat.
All tours in AK are expensive, but most are well worth it. Most all of the cruise lines use Allen Marine for water based tours - they have larger boats that can hold lots of people while the Orcas and Harv and Marv's have much smaller boats for a more personalized tour and often cheaper tour.
The same holds true for Skagway - check out Green Jeep, Dyea Dave, and Chilkoot tours.
Not sure what your kids would like, but there are things like Ziplines, white water rafting, bicycle tours and more. They might also like the bowling alleys and climbing wall on the Pearl. They might also be brave enough to go into the pools too - I prefer the hot tubs