knuckle pushups do work, but gradually. I've been doing them for over 10 years
I agree completely with the heavy bag hitting... they will toughen up your knuckles alot. Just be sure you are hitting correctly, - only the first 2 knuckles should be hitting (index and middle finger proximal joint, between metacarpals and phalanges, or 'hand-bones' and 'finger-bones' if you'd like)
After heavy bag, you can use something more solid like a makiwara - a leather striking pad.
Myself, I punch the wooden support column at my dojo. There are knuckle prints in it
strengthening your knuckles involves 2 things:
-creating callouses in the skin above the bone
-calcifying the bone itself.
The skin will become smoother and tougher, and the bones will grow in size to be able to take more of a pounding. This is a very gradual process - expect a long time before you see noticable results.
and it ain't pretty. my first 2 knuckles are big and red.