I would view the handgun option as a last resort. You buy a big bore (>0.40 caliber) and shoot with it. You need to be able to hit reasonably well at 10 yds. That is not too far and in an emergency, you're probably going to shooting pretty instinctively. So, practice is important.
If the trip is short. I'd make do with a marine 12 ga shotgun. If it is longish, timewise I'd get a handgun in addition to the shotgun. In southern Alaska, you will mostly be dealing with Black Bears or a possible irritated moose as I understand the distribution of game in AK. The 44 mag should be enough. Still kicks though. I would probably pack my 4" 41 mag revolver with solids since I don't own a 44 magnum revolver or a short barreled 480 Ruger. If you already owned a 357 mag, I'd carry that with the shotgun.
The more I consider this question, the more I would just take the 41 mag revolver as long as grizzly or brown bears aren't an issue. The long gun in a kayak is going to make it heavier and you will probably be carrying supplies too. Remember, you aren't hunting these animals, it is purely defensive. If you want to shoot some game for food, I'd take along a 22 rifle rather than the shotgun. I would wear the 41 (or 44) mag most of the time.