Duncan is the best by far, he's a top 5 all time player. Malone was good, no doubts about that, but he depended on Stock. When MJ or Pippen disrupted their offense, Malone wasn't great creating. For those that didn't saw Duncan in his first 7-8 seasons, he was by far the best Spur in 2013, when Manu and Pop throw away the 'ship in the dying seconds of the finals game 7.
It would make sense to have Dirk before Malone, since Dirk was able to get the job done. Kevin Garnett was never better then Duncan, not even during his MVP season. The 'Wolfs tended to pad his stats in blowouts and his game was less suited for playoffs.