When it comes to the motor coach, I wouldn't worry too much about the size of your camera bag, within reason. Unless you have some pretty ungainly gear, you should be just fine carrying your camera in your lap, with bag under the seat or in the overhead. You should assume that anything that gets checked into the main luggage compartments will be basically inaccessible during the day. All of the motor coach operators in Alaska will keep your time between rest stops to less than 2 hours: typically, they'll shoot for something closer to 1 to 1.5 hours between stops.

On board the train, there is no overhead storage and extremely limited luggage storage in general. This will vary somewhat between companies. I'm not sure about the luggage space on the Midnight Sun Express (Princess Cruises). The McKinley Explorer (Holland America Line) has some very limited luggage space on board its train cars, but that luggage is totally inaccessible during the ride. Wilderness Express (pretty much everyone else) has no luggage space on board the train cars. That said, the seating arrangement is quite a bit more spacious than on board the motor coach, or even on board commercial aircraft, so keeping a camera bag at your feet probably isn't a big deal. All of these operators have full-dome cars that sit somewhere between 16 and 18 feet high, with kitchens and dining facilities on the lower levels: hence the no luggage space. The absolute longest you will be on the train would be 8 hours, if you are traveling between Denali National Park and Anchorage in one leg.

I've worked for multiple of the major tour operators in Alaska for more than a decade. I started as a motor coach driver and am now a manager at one of them. Unfortunately, I do not have a lot of experience with the various flight seeing operators, and none at all in the Kenai Fjords area. My limited there experience suggests that you should be ready for a cramped cabin, but your mileage may vary by tour.

Hope that helps! Enjoy your trip.