“Get off the main street!”
I'll start with this. The main street you're familiar with "Takeshita-dori" is lame and commercial. Its definitely cool to check out, but its far from as you imagine it. It has become another hub for mass market junk and touts trying to sell you energy drink T-shirts and terrible snap-backs you can buy anywhere.
BUT! Cross the street at the end of Takeshita-dori. Stroll down an alleyway and you reach what I feel is a better representation of Harajuku. More strange fashion stores lurk down this way. More in line with clothes you might actually consider wearing too! Woo!
Also off the main street are many small cafes, bars and eateries. Situated all around the general area, these places range from "Eh, its alright" to "Dang son, I'm coming back here tomorrow". Which in my opinion, is pretty good.
Harajuku is more than meets the eye. Just please get off Takeshita-dori, that is not Harajuku. Its just a tourist trap!