Eddie, in my opinion, while pretty good in the ring, never came close to Benoit's level. Eddie became more of a character, instead of an overall great wrestler. Most of his matches in WWE were setups for his Lie, Cheat, and Steal gimmick.
Also, it can't be denied that Benoit held more titles, both in WCW and WWE. This to me, symbolizes both companies having more faith in Benoit. The only thing I think can be said in Eddie's favor is that he was the WWE Champion, while Benoit was World Champion. Although as has been stated, the World Title at the time was positioned as the more important belt.
I respect what Eddie did, and I do think he was a great wrestler, however he wasn't as great as he was made out to be after his death. He was presented as being right up there with Flair and Michaels as one of the greatest of all time. That was not the truth at all. Eddie was good, but not at that level.
Most people though will say Eddie was better simply because of the events of Benoit's final days. But you can't deny what he did in the ring, and even WWE has realized this. They'll never promote or talk about him, but they can't deny or forget what he did in the ring and what he meant to wrestling. Like I said, Benoit is most definitely the greatest technical wrestler ever, and I think he was the best period.