Sentence 1 can be better expressed with a have at the end:
I haven't known him as long as you have.
This sentence has essentially the same meaning as sentence 2:
I haven't known him as long as you have known him.
However, sentence 3 has a slightly different meaning:
I haven't known him as long as I have known you.
Consider that there are two people A and B, talking about C. In the first two sentences, B tells A that he/she hasn't known C as long as A has known C. However, in the third sentence, B says to A that he/she hasn't known C as long as he/she has known A. There's the difference.
Hope it's clear now!