Messi surpassed Gerd Muller's 40-year mark of 85 goals in a single year when he struck his 85th and 86th goals of 2012 in Barca's 2-1 win at Real Betis at the weekend.
Speaking ahead of Wednesday night's Copa del Rey tie with Cordoba, Vilanova told a press conference: "Leo Messi's great virtue is that he does as a professional exactly the same things that he did as a kid, and that's a difficult thing to do.
"Given who he is today and what there is yet to come, he is one of the greats in FC Barcelona history."
Next weekend Messi will line up against another of the world's leading strikers in Radamel Falcao when Barcelona face Atletico Madrid, but Vilanova rejected speculation that the occasion will see his star player driven to excel.
"Leo is always motivated, and I don't think it will be any special motivation for him to be playing against Falcao," he said.
Looking ahead to tomorrow's last-16 cup tie with Cordoba, Vilanova was refusing to take the challenge lightly given the scalp on offer to the second-tier outfit.
"It's a game people assume we'll win, but I'd have preferred to play a first division team," he said.
"It's the game of the year for them, like the Champions League final would be for us.
"Cordoba are excited about this because it's 40 years since they last played in the first division.
"This game will be very difficult. We will have to get a good result."