Very broadly speaking
Sitting = waverunner = big engine = fast = not very manouverable = easy
Standing = jeski = small engine = not very fast = very manouverable = hard
It really does depend on what you want it for, as transport the waverunners are fucking awesome, getting from one side of the island to the other etc, but for pissing around in a lake, its a jetski all the way.
Its kind of like comparing a honda goldwing and a motocross bike