The pontoons are super easy to drive. They are big and slow, but if you can drive a car (or a Sea Raycer) you can drive one. They just aren't as quick and nimble as the smaller boats. It is fun to all hang out together on one boat, but the action as far as driving the boat itself probably isn't as exciting with the bigger slower boat. Cast members help out with docking, so it is a really easy boating experience.
We did the pontoon with two of us, but the question of Whaler vs Sea Raycer comes down to how much extra room do you want. In the Sea Raycer the two of you will fill up the boat, and you won't be able to move around much, but you'll be nice and close. Someone who isn't as comfortable on the water might enjoy the extra space of the bigger boat. In the larger boats you can walk around and switch drivers too. The Whalers have a small bench for the drivers seat, which I believe can seat two, as opposed to the pontoons which have a captains chair. The Sea Raycers are cheaper though, so you could stay out longer. At the resort you can walk out on the dock and look at the boats and see which one appeals to you both at the time and then rent that one, so you don't really have to decide ahead of time.