Sorry to hear you got stuck.
The normal way to proceed is through the other side of the canyon where there's a cave entrance covered by grass.
But you can also skip the cave by jump over the canyon with a shotgun jump or a grenade jump if you've found the grenade launcher.
Are there enemies that can ride along your boat?
Yes the eeldogs (4 legged monsters) can jump on your boat. Fishes can also do that and they'll eventually die.
Thanks for the feedback, I'll be more mindful of things like that in the future.