While it's valid to rank any two albums relative to each other in that one must, by definition, be better, this not a particularly appropriate head-to-head comparison in that these two albums are not remotely similar even though the two bands that created them, when viewed in totality, are.
Piper is a psychedelic pop album made by a band that would later evolve into a prog band. In the Court is a prog album made by a pioneering prog band that would later distance itself from that genre by demonstrating that it was more versatile than the pretensions of prog would allow it to be.
That said, In the Court looms much taller relative to its surrounding landscape (early Traffic records and such) than does Piper. And while psychedelia carries much more cultural import than prog, this height advantage is too great for that to offset...may Syd Barrett rest in peace, but Piper is not even a Moby Grape or The Who Sell Out, much less a Sgt. Pepper's. So in this case, dominating the playground dodgeball game counts for more than does riding the bench on the varsity team. I voted for King Crimson. The awesome gatefold art doesn't hurt either.