Impossible, really, we could debate that endlessly. Today's footballers are developed using methods that get more out of them, and we know more about the human body, diet, and injury treatment. And as Scepticalscribe points out, players from older eras like Puskas (or Matthias Sindelar) are harder to evaluate - not to mention players from way back in the 19th century and first decades of the 20th. This is why almost all "best player" lists are dominated by players from the era of television.
Still, among the all-time top handful of players (like Pele, Maradona), Messi is not out of place. History will ultimately decide where he fits, but I am sure it will be near the very top of the pile - and in his case we have an entire career's worth of video evidence to support it.