Fernandes claims his current Portugal teammate and former United star Cristiano Ronaldo is the best to ever do it.
But Brazilian duo Fred and Telles pick their compatriot Pele as the greatest.
Answering questions from supporters on MUTV, Fernandes said: "We always fight because they [Telles and Fred] say Pele was the best in the history of football and I'm talking and I put Cristiano in the middle, of course.
"For me, Cristiano and Messi, I always say, both make history for many years and they were capable of being at the top for many years.
"And, of course, the same as me, they have never seen Pele play so they can't say he was the best because they never saw him. They say it because they're Brazilian and, in Brazil, they say it.
"I think Pele is one of the best in the world because I hear people talking about him and I've seen some history and some videos and you watch and everyone can see Maradona, Eusebio and people talk about Pele as being the best of all time.
"But, about Rivaldo, because we talk, we always fight about Rivaldo and Figo and which one was best. Who was the worst and who was the best.
"So, for me as a Portuguese, I always defend my players. It doesn't matter if I like them or not, I defend the Portuguese players every time. So this is a fight between Brazilian and Portuguese people but it is more of a joke than other stuff."