Barring any weight on album sales or mainstream, and simply concentrating on music quality throughout the nineties, I'd Neurosis more or less kicked the crap outta everybody.
From 1992's 'Souls at Zero' up until 1999's monumental 'Times of Grace', the band never released a bad album, only solid releases, and continue to do so today. Of course, Neurosis have never really been on the tips of everyone's tongue. Their music is very hard to grasp, but no band can really claim to be as cohesive and bludgeoning as Neurosis. And they've been doing this for 16 years.
After Neurosis, I'd say Emperor, although Equilibrium is a thorn in their side. ItNE and Anthems are enough to rule them worthy.
Opeth didn't get started until 1995, so half the decade is lost on them, although their best outputs do come from the 90's. But if the band remains intact throughout 2010, and the fanboys keep lapping up their subpar material, many will claim Opeth to own 2000-2010.