From the American Sailing Association:
"In short, if you receive any compensation, if the boat has auxiliary power, and if you’re operating in USCG waters, you MUST have a captain’s license."
So if the dive shop simply allows a random student to take over the boat, which eliminates the matter of consideration, they don't need a USCG licensed Captain. But if one of their employees is operating it...And their insurance may have something to say in the matter, either way. But of course you can always enquire at the Commandant's Office for an opinion from the folks who enforce the laws.
A pontoon boat just might mean they're in a quarry or other non-navigable body of water that is outside of USCG jurisdiction as well. In that case you'd only have to worry about state laws.