There's no question that some of the best VGM coming out right now is from the small-timer indie folks.
Rich "Disasterpeace" Vreeland is a chiptune allstar. His soundtrack for FEZ is very good, and the two arranged albums (featuring dozens of other artists) are very good as well (they are FZ: Sides F and Z respectively).
I reeeeally like the work of Alec Holowka. His best soundtracks are Aquaria and Offspring Fling!
And agreed on HyperDuck. They just keep getting better and I don't understand how that's possible. If you go back to "ARES" -- it's a pretty good rock soundtrack. But then Dust ... wowowowow. I'm still absorbing PAA4.
I'll also mention:
Jessica Curry's soundtrack for "Dear Esther" for those who like sparse, minimalist acoustic string kind of stuff
David Housden's soundtrack for "Thomas Was Alone"
Francisco Cerda's kick-your-face-in-with-amazingness soundtrack to the indie shmup "Jamestown"
Aivi Tran and Surasshu on the upcoming game CRYAMORE -- tons of music has already been released for it and the game's not even out.