Neutral Milk Hotel - In an Aeroplane Over The Sea
Probably about as good answer as you could get. Covers all the bases - Indie Label, Indie Music, Cult classic album (appears in most critics best of lists), Influenced the sound of Alt music into the 00's.
I'll throw in any 'Yo Lo Tengo' album - 'Painful' probably being the pick of their 90's output. Same with Sleater Kinney 'Dig Me Out'....and as a wild card 'The Crazy Gods of Endless Noises' album 'Heavy Planet'.