From my experience (when it comes to knee pain and cycling, I unfortunately have a lot):
First, this is a complex problem with many possible causes. See a physiotherapist or sports physician and identify the problem!
Second, spinning is good advice and all, but bike fit is actually a lot more relevant to knee pain. If your current fit causes your legs to move in a pathological way, all the gearing down and spinning in the world won't do you any good; and if you get a good fit to your bike, you may well be able to pound away on the pedals (within reason) to your heart's content without inflicting injury.
Third, do not just assume that your saddle is too low and keep raising it if pain continues. A too-high saddle is actually a very common source of injury, partly because cyclists are hyper aware that a low saddle can cause injury and overcompensate for it. Get an experienced bike fitter to check you out! And be careful - I had an inexperienced fitter that set me back literally for months or years because he had me raise my saddle when the problem was that it was too high to begin with.
Finally, rest and give your knees time to heal. That means time off the bike. You need any inflammation to go away to actually know if you've fixed the problem. Be patient. Knee injuries are slow to heal because of low blood flow to the area.
Good luck!