Same thing happened to mine. I used a hole saw to cut maybe a 1" hole in each pontoon and I seal them with an expansion plug, basically a rubber stopper with a bolt through it. Holes are above the waterline, but they are lower than the drain plugs already in place. Tighten the bolt and the plug expands to fit the hole. Just buy the right size plug at any auto parts store.
I do like the idea of the aquarium pump, just never thought of that. Saves holing the hull, but those plugs have never failed me!