If this question were to be answered prior to 2010? I'd have said Patrick Willis. While both have improved since, I think the answer.. still very close... but I'd say Justin Smith. When Justin first arrived back in 2008, I'll be honest... I wasn't so sure he'd fit right in as a 3-4 DE. Many of times, he would lack discipline in attacking the QB and give up his run assignments. He needed time to bulk up more to anchor the run game also. He sure did level out on all aspects of his game as the years progressed, and now, he's obviously just off-the-charts valuable to us.
Nothing against Sir Willis either. Both are incredible players... both belong in the top 10 of all defensive players.