While I have never been to Alaska, I have been rafting and kayaking for ~19 years and many of my friends have rafted, kayaked and canoed in AK and Canada. All of the water is extremely cold, sometimes in the 30's depending on location. Those temps are extremely dangerous. Survival time in water that cold, without a drysuit or other exposure protection, is literally 15 minutes or less. Unless you are an expert kayaker with a ton of paddling experience and are fully prepared to self rescue I would advise against taking the kayak out. I have been in 52* water in the Grand Canyon on a mile long swim after a flip and without the help of my fellow rafters I am not sure the outcome would have been as positive as it was. Hope you have a great time in AK!
RichH