I often go down to San Pedro for long periods of time, and take super sized luggage (2 pieces), an extra large carry-on suitcase, as well as, a huge bag that constitutes as a purse.
Never any trouble taking the puddle jumper . . .the carry-on suitcase rarely gets to go with me in the cabin, but I'm allowed to take it to the plane myself, and they put it underneath while I watch.
From time to time, but not that often, my larger luggage arrives on a different plane. Haven't lost a piece yet, never been charged for extra luggage or overweight . . . which is certainly something I can't say for the international carriers.
Take the plane, don't worry about your luggage with the puddle jumper.
Seems to me, you'll have a lot more trouble with all that luggage, trying to take the water taxi.