I love the Spider-Man gallery of rogues in general, so I thought Vulture and Mysterio were both great. It's hard to count Willem Dafoe as an MCU villain, but he was great, too.
Beyond that, the top three for me are probably Loki, Thanos, and Killmonger.
https://imgur.com/WqDcNNq
https://imgur.com/89Z5jrB