Messi received the award after Argentina lost 1-0 to Germany in the final but he looked far from happy as he went up to collect the trophy.
"I could see he didn't want to go up and collect it," Maradona said on his television show "De zurda", adding that "marketing people" had made a decision he described as "unfair".
Maradona led Argentina to the World Cup in 1986 and was named the tournament's best player, but although Messi scored four goals in the group stage he failed to find the net in the knockout rounds and was subdued in the final.
FIFA president Sepp Blatter also expressed surprise at the choice on Monday which was made by the football governing body's technical study group.
"Shall I be diplomatic or tell the truth, OK the truth...I was a bit surprised he was the choice but his goals were decisive at the start of the tournament," Blatter told reporters at his final media briefing of the 2014 World Cup.
Argentina coach Alejandro Sabella, however, backed the decision to give the award to his team's captain.
"I think he did deserve it. He played an extraordinary World Cup and he was a fundamental factor to our team," Sabella said.
Maradona, who said Colombian midfielder James Rodriguez should have won the award after scoring six goals in Brazil, was happy with the overall performance of the Argentina team.
"We raised our flag high, there's no doubt about that," he said.
"Germany won due to a misunderstanding in the defence, but at no point were they better than us. They showed us a lot of respect and our lads earned that out on the pitch."
