Videos ceased to matter much at some point in the 90s. I mean, they still mattered, but not as many people watched them because MTV quit playing videos 24-7. Since they were at their apex from about 1982 to 1992, the answer pretty much has to be in that time frame. And yes, Thriller is the obvious winner. I hate to sound old, but I wonder how many people here actually remember MJ at his apex. Thriller was THE ALBUM for about 2 years straight. He was the biggest thing since Elvis, a transcendent entertainer. His commercial was a big deal. His hair catching on fire during the commercial was a big deal. His tour, which was a reunion tour with his brothers, was a huge deal, with multiple performances at sold out football stadiums to accommodate the demand. They did three at Arrowhead (not to be confused with Arrowsmith-- Jesus H. Christ, RJ) to open the tour. Thriller was pretty much the last song from that album released as a single and the buildup for the world premiere of the video was still enormous, even though the album Thriller had been released more than a year before and everybody knew the song in and out by then. Having a long video like that was something new too, and something nobody has really pulled off since. Bowie did it with Blue Jean the next year, but it wasn't nearly as cool. Thriller wins this running away.
Sledgehammer is a good #2, but that can be debated. Money For Nothing was a big vid too. Robert Palmer's Addicted To Love. Pretty much any Madonna from Like A Virgin through Vogue (Like A Prayer was highly controversial with her seducing black Jesus). I Want Your Sex was also hugely controversial.