Last fall I had a problem with swelling under my knee cap, and if I ran, it would either numb out or hurt to where I could no longer run. I talked to a knowledgeable trainer about it, and he explained what was causing the pain etc; further, he said in order to cross train effectively, I would need to do activities with small range of motion of the knee. That being said, I could not ride my bike, and I was left to the elliptical.
Just take some rest and maybe the bike will work for you, but if it hurts at all while riding, then you might as well be running. I waited until too late by trying to train through it, and ended up suffering early in the cross country season. Take some ibuprofen to cut down the swelling, ice often, go on some long walks to help promote blood flow to the area, and I got this Arnica cream and wintergreen oil from this kind of hippie-holistic health store (I was desperate), yet I got over it and put together a decent season. Best of luck man.