Ronaldo is also a five-time winner of the prize, but has not been as prolific since joining Juve from Madrid in 2018.
However, Villas-Boas backed his fellow Portuguese, although he labelled both Ronaldo and Messi as extraterrestrials.
"It's difficult... I am Portuguese so of course I support Ronaldo more," he said.
"Cristiano took a risk by leaving the best team in the world, with more titles in the world. That kind of risk should be appreciated. Playing in Italy and scoring goals is difficult.
"Messi is still in his club, Barcelona, which is a big club. He is able to make the difference.
"But I am more for Cristiano because I'm Portuguese. Both of them are exceptional, it's difficult to choose. It [Ballon d'Or] will become a competition between them.
"Having these two players in the same generation and watching them is absolutely incredible. They are extraterrestrials."