Which boat is funner and has better theming?
I personally prefer the Mark Twain Riverboat, but which one is better is a matter of personal preference. The Mark Twain Riverboat is an authentic paddle steamer and arguably offers better views due to the higher observation deck. There is also the opportunity to ride in the wheelhouse with the pilot. Sailing Ship Columbia is a recreation of an actual ship, but it is motorized and doesn't use sails. However, the ship does feature a museum below deck and there is an authentic cannon on board that is fired during the trip.
I'll vote for Sailing Ship Columbia, perhaps in part because it doesn't usually run whenever I'm at the park (it only seems to run on crowded days). As AJ said, it has the below-decks explorable area, which I find amazingly immersive. A captain's office, the crew's galley, barely any people at all, you forget you're in Disneyland! And the on-ride audio is a selection of old sea shanties ("Blow the Man Down"), which rouses the soul. But yes, if you need shade or seating, do the Mark Twain. (Incidentally, I rode the day's last Mark Twain recently in full nighttime, and that as amazingly transportive as well!)
I was always a Mark Twain guy, but recently took a trip on the Columbia. I loved it. Standing on the back of the ship and seeing the world drift by while also seeing the ships masts, ropes and other rigging in the foreground was extremely pleasing. I think the main reason I had avoided the Columbia was the lack of shade. Trust me...it's worth it.
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I have only been on Mark Twain Riverboat, but I think it depends on the person. Kids prefer Columbia due to how it looks like a pirate ship, but adults like Mark Twain due to all the shade.
However, I am not really a fan of Rivers of America. I always found it on the boring side. I wish it had more animatronics.