saddle height and cleat alignment are the two most common causes. try to adjust your cleats so that your foot is neutral, this may not be the same on both sides. do the eggbeaters have float? you might benefit from this feature in different style cleats.

watch any number of videos on youtube for saddle height adjustment, but the general rule of thumb for me is that top of knee pain is saddle too low, below knee pain is too high or not setback correctly. play with it a little.

also, rest! seriously, take a day or three just off the bike. you cannot heal while you continue to strain. and continue to use your brakes instead of resisting with your legs as much as possible, as this will lessen the strain on your connective tissues. good luck!