For me, based on my own personal preference, I’m going with Archers of Loaf, with The Sea and Cake a close second, and Pavement, PJ Harvey, and getting some strong consideration.
Archers of Loaf put out music that consisted of some of that quintessential 1990s post-punk indie-pop sound but also had a distinctive sound with the way Eric Johnson utilized his lead guitar playing. Frontman Eric Bachmann had (and still has) a commanding voice that grabs your attention. They absolutely rocked and put on a great live show. They put out four full length albums in the 1990s, three of which were fantastic and the last of which was solid, though not on the level of the first three IMO. They also put out a brilliant EP between their first and second albums and a really good collection of b-sides and unreleased tracks.
The Sea and Cake put out great album after great album over the course of 25 years between 1993 and 2018 (not sure if they have more to come), and may be the most under-appreciated band ever. And the four albums they put out in the 90s were great. The Biz, released in 1995, may be my all-time favorite album. They put out some very chill rock with jazz-influenced guitar that I could listen to all the time.
Pavement was sort of the quintessential indie rock band that influenced so much music of the era (and beyond). Though their sound was always recognizable, they evolved from each album to the next, putting out five full-length albums between 1992 and 1999.
PJ Harvey has been constantly reinventing herself with each album and has been doing it for nearly 35 years now. Her output in the 90s was consistently great, while also being dynamic, and after the drastic shift in both sound and image in 1995’s To Bring You My Love, it was exciting to wonder where she would take us next.