New Jersey has had a fantastic record through the 90's. They've been producing about 3 regular NHLers per year during most of that time frame. The one complaint that I would have with their drafting is that I think they've trailed off in the past few years. In the last 5 or 6 drafts, there doesn't seem to be the same returns as they've seen in the past. Zach Parise is of course a great acquisition, but, it's pretty slim for the rest. Paul Martin is a solid pick-up, but, that's going back to 2000. To be fair, I'm not familiar with Jersey's system, so, a lot of the names I'm looking over may be on the verge of making it to the bigs.
If you look at the 90's as a whole, I don't think you can find a better record. Ottawa is definitely competitive with it. We also have been producing about 3 NHLers per year. We've drafted 7 top-end talents (Yashin, Demitra, Alfredsson, Spezza, Redden*, Havlat, Hossa). Three of those players came from high picks, so, reduce the number to 4, if you'd like. New Jersey has produced three top-end talents (Brodeur, Nieds and Elias).
As for saying which team is better, honestly, why bother. Both teams have done an incredible job during that time frame, that, I don't think the fans of either team could ask for anything more from management. The only complaint is that perhaps New Jersey's record may be faltering a bit, without matching their previous success.
As an Ottawa fan, I've been highly encouraged by what I've seen from Meszaros, Eaves, Emery, Schubert and Bochenski, all recent picks, and, there's still big expectations from Kaygordov, once his Russian contract expires. That's what I've liked the most about Ottawa's drafting, it has survived transition. We've gone through countless GMs, different heads of scouting, etc., yet, our drafting record has remained impeccable. I was really worried once we lost Jarmo Kekailenen as our head scout, but, the organization marched on, and has succeeded without him. Meanwhile, St. Louis (where he went to) hasn't done anything remarkable on the drafting front. I guess he never played a big a role as we thought.
*Since Redden was acquired with a swap of the first and second picks, I see that as the organization just doing a do-over of their draft pick.