Indie rock is auto-produced and has influences both of big and minor bands/musical genres, it's part of alternative rock
alternative rock is a bigger genre that contains all genres that diverge from the (current) mainstream, like avant-garde rock,experimental rock and new wave
that's how I remember it, dunno if the terms changed in the last decade or so
I can try to put a definition on it (to me, indie is a drier, less affected, more straightforward sound, something like the Strokes, Yeah Yeah Yeahs, or the Kaiser Chiefs), but most people use them either interchangably or to mean a group on an independent label. Of course, some of the biggest bands in the world are on "indie" labels, like XL, so the term is meaningless now.
Alternative is a much bigger genre, anything that doesn't comfortably fit within the context of modern rock or classic rock. Alternative can mean Pixies (surf punk), Shellac (math rock), My Bloody Valentine (wall of noise shoegaze stuff), R.E.M. (jangle pop), Minutemen (funk punk), and so forth.
Problem is, alternative is modern rock. With rock falling out of favor in the mainstream for hip hop and electronica, no longer do you have your big pop rock crossover artists (the Springsteens and the like) and then the weird underground. Rock artists don't just play loud music with guitars or quieter music with guitars. They're doing shit with electronics and drum machines too. The alternative is now the mainstream, so it's all up in the air.
Tl;dr indie is a drier and scrappier subgenre of alternative, which isn't one genre but a whole bunch. Alt is now mainstream anyway so the distinction's pointless. Yes, it's confusing.