Pippen was the 2nd to 4th best player in the league for a large part of the 90's. He was probably the best defender in the league for much of that time too. Pierce was never a top 5 player in the league at any point in his career.
I love Paul Pierce, but he just wasn't as good of a player as Pippen. During the Dream Team Olympics, I read a column that the two best players on that team, at that time, were Jordan and Pippen, because both were in their prime, had tremendous chemistry together and were the two best defenders on the planet.