I have it too, though running is much harsher than cycling on my knees.

The usual advice - saddle height + cadence applies but I want to add that with clipless pedals you can also experiment with cleat position. I like mine further back than the default "ball of foot" position. I'm also very sensitive to saddle height. I have about 5 pairs of shoes with cleats, and I wish they were all the same sole height (but they're not). I (think I) can feel the differences between them.

And I always prefer using clipless, regardless of ride distance. I stopped using toeclips once I went clipless.