Motown 25 is legendary. To me, that will always be his best Billie Jean performance. Those couple of minutes magically captured Michael's transition from child star to superstar. He went from a boy to a man at literally the drop of a hat. Brilliant.
Concert-wise, I love the Optimum-produced Victory Tour version of Billie Jean because it captures the essence of Michael Mania as it was in 1984. He was at the height of his career in America and could've been elected president had he ran for office.
Another outstanding, underrated BJ performance is Yokohama '87. Often overshadowed by Bucharest (and Sheryl Crow's voice lol) but I really love everything about it. His dancing is amazing and he does the circular moonwalk which he basically downgraded in later performances and tours. To me, Yokohama's Billie Jean is superior to Wembley's in terms of singing and dancing and the music has more groove to it.
Bucharest is a great performance as well but it's just that. There's an insane energy during that entire concert but less overall "magic". What really stands out is the atmosphere and the picture/sound quality. When you watch it, it's like you're there. It's (along with Munich '96) probably the closest to HD we have of Michael's.
And don't get me wrong, every Billie Jean performance is brilliant in its own right and it's hard to choose one over the other. I'll find something amazing or likeable in any performance of his, regardless of which tour it is but I personally digg the rawer versions of Billie Jean in which the routines are less polished and less common in terms of concert use.