Maybe I don't scout games as closely as some, but that's kind of hard to prove in any quantifiable way. I'd certainly agree that at his peak, Warren was likely better than Ellis is now. But Warren's peak was a long time ago. Ellis certainly was and is a superior pass rusher. Even Ellis' total of 4.5 sacks last season was better than all but one of Warren's seasons. Ellis also has a high of 12.5 sacks vs Warren's 7.5, and more than triple the career sacks with only three more seasons in the league.
Interestingly, the Jets run defenses have been consistently superior to our own for the duration of Warren's career as a starter, at least as far as YPA is concerned (2006 being a notable exception). Since Warren benefited from Wilfork and Seymour beside him, and we know those dudes weren't the weak the link, could an argument be made that Ellis was likely the superior run stuffer as well? Of course, the Jets haven't exactly been playing from ahead as much as we have the past decade. I would imagine run stopping suffers a tad in prevent defenses.