A Waverunner and Jet Ski are the same type of personal watercraft.
But Waverunner is a brand name and a Waverunner can also be other types of watercraft that the company and manufacturer Waverunner makes.
But most people do refer to a Jet Ski as A Waverunner and they're right when they're mentioning a Waverunner as a Jet Ski because there are Waverunner Jet Skis.