So i read this article on t-nation
Testosterone Nation - Total-Body Training
and I like the routine but I am wary about lower body excersizes... (i had knee surgery about a year and a half ago, and i feel good with it, i mean i play catcher so i am pretty confident in it... but i am worried about heavy lifts and stuff while squating)
so is there another lower body and hip/back excersize that i dont have to do squats for?

The reason for the squats is that it is compound movements, im currently doing that same routine...Not sure there is another compound movement excersise for legs that works quite like the squats, but if you feel your going to injure yourself, perhaps you may want to consider a different routine, or wait some time while you fully heal.

What does your doctor say about it? physical therapist?

sometimes you have to go easy for life, sometimes you're 'as good as new' and can do squats.

nothing is as good as squats.
leg extensions actually have a greater potential for knee injury. ditto for leg press. smith squats too, really any machine squat won't have the same identical movement and will cheat you in some ways, and possibly hurt you in others.