In addition to the advice to decrease your gear and increase your cadence, there are a few other things to consider that may help relieve the knee pain:
1) Your distance from the pedals should be such that you have a bit of a bend in your knee even at full extension (pedal at it's farthest point from your body) AND not less than a 90 degree bend relative to your upper leg when the pedal is at its closest point to your body. In other words, when the pedal is closest to you the angle at the back of your knee between your lower and upper leg should never fall below 90 degrees (at most; if it's greater than 90 degrees, that's even better).
If your recumbent and crank arm combination are such that you can't get your leg to have a slight bend at full extension while also avoiding a less than 90 degree bend at minimal extension, then err on the side of the minimal extension. Set yourself up to avoid a less than 90 degree bend in the knee at the expense of a fuller leg extension at full pedal extension. Having your knee continuously bend to less than 90 degrees puts a great deal of stress on that joint when it attempts to re-extend out from that position. Better to sacrifice a little power as a result of not getting a full leg extension than to sacrifice your knees.
2) I rode diamond frames for a long time without knee issues. When I switched to a recumbent, I did experience knee pain despite spinning low gears and using the same shoes, same pedals (transferred right off my diamond frame bike), and same cleat position. After doing a little research I tried the suggestion of moving my foot forward on the pedal so it was now in front of the pedal spindle (as opposed to the traditional recommendation of "ball-of-the-foot-over-the-pedal-spindle"). This eliminated my knee pain.
Good luck
