I voted for the canoes because they are so unique from anything else at a Disney park (or any other theme/amusement park for that matter). So if you really are just going to pick 1, that’s what I would do it for. The River guides on the canoes are just as funny (if not funnier) than the funniest Jungle Cruise skippers and even though you are doing the paddling to get you around the river, it’s just a lot of good fun (and a very good arm workout).
However, the Mark Twain is my favorite for its beauty, the ability to relax & just soak in the views of the Rivers of America as you pass (and wave to people) and the historical treasure that it is to the park (Walt & Lillian celebrated their 30th wedding anniversary just 4 days before Disneyland opened on a party held on the boat as it cruised around the Rivers of America). If you have the option of doing a sunset/after dark cruise along the Mark Twain that is even more serene & beautiful. And I would highly recommend doing this in addition to the canoes if you have the option (the Mark Twain has to run late enough for it to get dark which means it has to be a night that F! isn’t scheduled and the Mark Twain has to not go down before dark- it’s struggled more as of late needing more down-time than it used to so it may not be able to stay out as late anymore, but it’s beautiful when it does).
And then, to also throw some love to the SS Columbia, it’s by no means my favorite but it is still pretty cool & below deck has quarters setup how living quarters on a ship in the 19th century would’ve been so an interesting museum-like area of it that is really fun to explore as well giving you something different than either of the other 2 above.
So really, if you have time there’s enough interesting about each one to merit trying them all, but if you really just have to absolutely pick one- Canoes. (But Mark Twain is beautiful so I would make time for it at least once over repeats of other rides/attractions).