I agree, they are messy little guys. They are a lot of fun to watch though.
I think, however, that between the Gobys, Corys and shrimp, most of the food the puffers make a mess of gets cleaned up pretty quickly. I rarely see old food in the tank more then an hour after feeding.
I suspected that overfeeding could have been causing the algae.. So before a week long vacation this summer I cleaned up as much of it as I could from the parva.. Came back a week later, algae was back and the fish hadn't been fed for a full 7 days..