The Argentina international has scored 14 goals in his last 10 matches for City in all competitions and is the top scorer in the Premier League this season.
After scoring twice in last weekend's 6-0 demolition of Tottenham, Pellegrini described him as one of the top performers in world football, behind only Messi and Ronaldo.
"I said last week after Messi and Cristiano Ronaldo he is the best," the Chilean told reporters. "Both are not playing in the Premier League so he is [the best in England].
"He is a better player because he is older.
"He arrived in Spain when he was 18 or 19 years old. He was always a very important player, a top player, but this year he is trying to work a little bit more without the ball.
"Three or four goals of the last goals we scored are because he is doing a good job pressing their defenders.
"I think he is more complete."
Aguero arrived at the Etihad Stadium in 2011 and has netted 45 goals in 75 Premier League appearances, including the goal that sealed the title for the club in 2012.