The 68-year-old has voiced his admiration for the Blaugrana star, while he also paid tribute to the form of Cristiano Ronaldo and Franck Ribery in the past two years.
The Argentina international, 26, missed out on a fifth Ballon d'Or trophy earlier this year as Real Madrid's Cristiano Ronaldo scooped the award, yet Heynckes is adamant the prolific attacker should be regarded as a legend of the game.
"Messi has swept the board at the Ballon d'Or in the last few years. He's a genius and is certainly on a par with Maradona and Pele," Heynckes told the official FIFA website.
The 68-year-old was equally full of praise for Ronaldo, while adding that Franck Ribery has drawn close to the level of the world's top two with his performances and team ethic at Bayern Munich in the past few years.
"The way Cristiano Ronaldo plays is incredible. He's so strong physically and is dangerous in front of goal - he's another absolutely unique player," he said. "In the last two years Ribery has become a real team player at Bayern. He has huge individual talent when it comes to creating and scoring goals, but maybe not to the same extent as Messi and Ronaldo.
"However, he's learned to help out in defense and to play for the team. I think our success boiled down to that last year, the fact we played superbly as a team. Ribery fit perfectly into that system."
Ribery finished third in the 2013 FIFA Ballon d'Or race behind Ronaldo and Messi.