The rankings on www.eurotopfoot.com showed the Argentina striker had amassed 68 points, 10 more than his closest rivals Didier Drogba of Chelsea and Antonio Di Natale of Udinese who scored 29 each.
Messi netted Barca's third and fourth goals in a 4-0 victory over Valladolid that delivered Barca their second consecutive league title on Sunday.
NEWS:Barca retain league title
"Messi is the best I have ever seen, of this there is no doubt," Guardiola told reporters on Sunday.
"As well as being a winner he has great ambition. At 3-0 up, with the league in the bag, he continued chasing as hard as anyone else. He's impossible to emulate."
His haul of 34 in the league matched the club record set by Brazilian striker Ronaldo in the 1996-7 season, when he also won the Golden Shoe.
Atletico Madrid's Uruguayan striker Diego Forlan won the shoe last season with 32 goals.
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