While I suppose it's possible to take a pack animal in a canoe, I think you'll find it's probably better to just tie everything up in a tarp and put it in the bottom of the canoe.
(Canoes are... a whopping 50gp according to Tomb of Annihilation. They also hold up to 6 people, so we're talking some pretty big canoes. Looks like this little group will only need one of them.)