I'm still sort of a newb to Asian music. So will take your word on that. I've run across a number of pretty good indie and alternative performers in recent searches though, mostly in the K-pop and C-pop genres (because J-pop searches are still a bit difficult for me). So they are possible to find, if you're willin to dig just a bit.
Although they don't get as much play on the mainstream shows and charts, several of the smaller, and even a few of the larger Korean music labels include indie and alternative artists in their rosters. Mirrorball Music is one of the more prominent independent labels. But you can find some pretty good alternative-ish music/artists on some of the other more prominent labels as well, like 1theK, CJ E&M Music and Super Sound Bugs!, for example.
SM Entertainment also distributes some more creative and collaborative work via its SM Station digital music project (as you probably know). I wouldn't describe most of the SM Station tracks as "alternative". But it allows some of the label's more talented artists to stretch their legs a bit, and experiment with other styles and genres, which is a good thing in my book.
Lim Kim and Gain (of BEG) were a couple of my early favorites to bring a more alternative vibe to the Kpop genre. Following are a few of the more recent tracks that I like though, by a variety of artists. All female, for the most part...