The Breeders — not the biggest recorded output in the 90s (or since), but influential and absolutely classic stuff. Pod is the album for the cool kids, Last Splash is the summertime trip to the county fair where you have a great fuckin’ time.
Kathleen Hanna had three projects in the 90s — Bikini Kill, Julie Ruin, and Le Tigre. I can see an argument that all are in some way dated or too idiosyncratic to have “stood the test of time,” but there are some great bangers on those records and they certainly influenced a lot of later musicians.
Cat Power — made her bones in the 90s and released one classic album in the decade, *Moon Pix. *I hear echoes of her style in lots of (often kinda insipid) singer-songwriter stuff today. I’m glad she got sober in the 00s for her sake, but I can’t say I appreciate what it did to her musical output. The Covers Record came out in 2000, but it’s pre-9/11 so maybe we can add it to her tally there.
I’ll be specific and also nominate only the 1990s incarnation of Belle and Sebastian, when Stuart Murdoch was in the band. Those three albums, and If You’re Feeling Sinister in particular, just scream 90s sensitive-guy indie music to me.