I think the first half of the Nineties had a good identity: Grunge Alt/Rock and Gangsta Rap. The latter half of the decade gets far more hit or miss with me, with much of it having quickly faded from my memory (weak radio fodder like Semisonic comes to mind, and then that unfortunate fake 'boy band' craze).
Radiohead seems to be caught between the 90s and the 2000s. Pablo Honey was maybe 93? A nice album but nothing great. But "The Bends" ('95) was the beginning of something transformative. Not as big of a shift in the musical scene as, say, the one Nirvana created; but it influenced bands to come. And "OK Computer" ('97) was brilliant! (And probably influenced even more bands yet!) So I'm tempted to vote for Radiohead, but I'd feel more certain about it had "Kid A" come out in 1999 instead of 2000.
Y'all made good points about Blur and Pearl Jam, too. I could see either of 'em. Though, I'd give the nod the PJ.
And I'd never listened to any of Flint's "Jellyfish". But I kind of liked it. Reminded me of a more modern-sounding Queen at times with a touch of Beatles thrown in (or maybe just some of the many Beatles-influenced bands). I'm going to add it to my list of CDs that I might someday buy.