The smallest airport I've ever been to is found in Madurodam, The Hague.
For airports where I've actually boarded a plane, I think KDL would be a good candidate (10.000 pax annually, maximum of 2 daily flights on a Jetstream 31) although VDB is smaller in terms of pax (just about 4000 annually. Also at maximum 2 daily flights on a Swearingen).