Vegito was able to overpower a universe buster in Super Buuhan. Thanos was able to stand his ground against Galactus and the entire Avengers.
Speed wise, they match up equally. And in strength as well.
The only advantage I give Vegito is his superior energy projection. Vegito will win because of that.
@justanormalguy: It's not really underestimating in this case. Vegito is up against Thanos. Thanos has managed to survive powerful attacks from Galactus and even managed to put up an impressive display against Odin and keep in mind that Odin mopped the floor with the Silver Surfer who is an immensely powerful being.