I went kayaking in Juneau a couple of years ago. It was terrific. There were mostly 2-person kayaks, and the water was calm. We were within sight of Mendenhall Glacier the whole time. We paddled around for an hour or more, with a guide, and saw seals and other marine animals that I can't recall right now. Once back on shore, we had cider and snacks before the ride back to the ship.
I've never been rafting, so I can't speak to that.