"It's just not as close to the surface as it was in the early days of the internet or BBS."Precisely. I'll add that today that 'underground' is a very small (yet important, if not critical to its future) part of the whole internet whereas in the early days it was most of it; hence the appearance of it being farther from the surface.
No need to reach for Tor, take HN whose volume is certainly much lower than those Facebook streams and various LOLcats, yet it is certainly pivotal to what's actually built on the internet. The next Facebook won't come from its users, it will come from one of you.
Human-Computer interaction as envisioned is at its peak. Dare you tell me that Second Life, World of Warcraft, or Eve Online are not quite akin to the metaverse that was envisioned in Snowcrash. Tell me that those robotic prosthetic limbs are not close to what you see in Gunnm (Battle Angel Alita in the US). All those eyes, ears, and even memory prosthetic devices (http://www.newscientist.com/article/dn6574) seen in Ghost in the Shell and Johnny Mnemonic are not dreamt of anymore, they are very real and useful to many (although admittedly they did not reach such levels of advancement, but that's a matter of time). Tell me those efforts to control and monitor everything including the internet "for the safety of everyone and his dog" are not dystopian in many ways, and get a look at how the third and fourth world are manipulating technology in ad-hoc, cheap, creative and dangerous ways to try and follow us in our first-world countries steps.
Of course there is some error correction to apply with regard to what was envisioned before all of that was even remotely possible; it is no wonder that fiction varies from reality.
Cyberpunk lives, for the best and the worst, today.