You really need a sewing machine with a quilting foot on it to do it well, though you could do it by hand if you've got a lot of patience.
1. Take a piece of fabric patch material that's 2" longer and 2" wider than the hole.
2. Fold over each edge so there's a 1/2" overlap on each side. You can use some pins or paper clips to hold the material folded and then iron them to set the fold. Once you've got it pretty well folded over, remove whatever you're holding it with and iron it one last time. Use a piece of cloth in between the patch material and the iron since you'll probably end up using nylon for the patch and the iron can melt it pretty easily!
3. Apply Aquaseal liberally to both the patch and pontoon and then squeeze them together. Use a large metal spoon to smooth out the excess Aquaseal and any air bubbles.
4. Place a couple of phone books or something else similarly heavy on top of the pieces and let them dry overnight.
5. Sew the two pieces together with double rows of stitching around the outside. Make sure you go through both pieces of the doubled over patch on both rows of stitching.
My passion for catching fish is eclipsed only by the fish's passion not to be caught.