The LHC is basically working at the same energies equal to cosmic rays striking the earth's atmosphere.
Within a factor of a few tens of millions, you are right.
Nope, GP was right. The centre-of-mass energy in collisions of UHE cosmic rays with our atmosphere is of the order (slightly above) of the centre-of-mass energies reached at the LHC. That's another reason why we build colliders: it's hard to reach high energies in fixed-target collisions.
You'd think that after 4.5 billion years of cosmic rays hitting things like this planet, the sun, the other planets, etc. that a black hole would be here by now.
What about speed relative to the earth? A black hole produced from a cosmic particle will be produced from a stationary particle being hit, and will thus have a high momentum, easily enough to escape the earths gravity well before interacting with anything. A black hole produced at CERN will be produced from two particles travelling at nearly the same speed in opposite directions, so it will be travelling much slower. Or will it still have a high enough speed that it doesn't matter?
Don't forget that the LHC is colliding the quarks and gluons inside the protons, and the speed (momentum, you mean of course) of the incoming particles is never mathematically equal. Still, you have a valid point, this is an important difference between the LHC collisions and the comic-ray ones.