Pain that bad is a big signal that something is wrong. The areas you describe are your quad tendons. Back off, let it rest, let the inflammation subside. Ice and antinflammatory meds may be in order to calm things in there. You need to evaluate your training and why your knees now hurt this bad. Do this before it progresses to something possibly worse. I have been there. In my case, I had chronic knee pain in that very spot for quite some time. I ended up with ruptured quad tendons from not listening to my body. I found out from my surgeon I had micro tears in both tendons from pushing too hard all the time. He said it was just a matter of time. Don't do what I did.
crap i was affraid it was more serious then i thought. would msm powder and Glucosamine sulfate help as well as icing and antiinflammatory?
I think that may help also. Allow some time though. If it is your connective tissue giving you the problem, they get very little blood supply unlike muscle and take much more time to recover.
Do you go heavy and below parallel on squats?
ive stopped doing squats for a few months now because i was getting the same pain. when i was doing squats i always went heavy but no lower then 7 reps a set and went as low as possible way below parallel. i just cant believe this happened i do all sets very controlled.
crap i was affraid it was more serious then i thought. would msm powder and Glucosamine sulfate help as well as icing and antiinflammatory?
this might not make sense to you, but the glutes control the knees. meaning, poorly funtioning glutes will make your knees hurt eventually. even if you have well developed glutes, that doesnt meant they are functioning well. i would start doing glute activation exercises like glute bridges for a few sets of around 10 reps before things like squats, lunges ect to try and get them working well. dont forget about glute med as well, do some lateral band walks as well. i would hop on a foam roller and work your IT band, hip flexors, quads, hamstrings and glutes as well.
edit: also, if you want my honest advice...get the hell out of the leg press, you're not getting any glute activation in that damn machine. you want fully developed legs???? squat, lunge, single leg squat and RDL...there you go big man