Bit.Trip Runner is an excellent game, so I can definitely recommend that. The other Bit.Trip games in that collection are very solid as well, so $15 is a pretty good bargain.
Having said that, somehow HarmoKnight has slipped under my radar until your post made me look into it, and after watching a few videos on YouTube, I've literally pulled a muscle in my neck because of how quickly I reached for my 3DS. So, I can't say for certain, but HarmoKnight looks pretty cool, too.
I've really only played runner 2 and some of bit trip beat so i can't really vouch for them but i gotta say harmoknight has been lots of fun so far. It's short in case you haven't heard that but there's a good number of stages that you can play on normal or fast speed and it's so super charming.
Definitely Bit.Trip.Runner. I just played the demo of HarmoKnight - the 2D artwork look great, but what I played didn't seem anywhere near as good as BTR (I ended up quitting after it became Quick Timey).
Anyway, the main difference between the two is that HarmoKnight is more about being in time with music, BTR is more about learning a by trial and error.
I know this is a little late, but this game is really good and I urge people to give it a chance. I have not played Bit.Trip. so I can't speak to the quality of that, but HK is a very cool game that has a few spins to the genre and even has some cool Pokemon themed levels.