The generally accepted explanation is a phenomenon known as cavitation. Pulling apart a joint generates negative pressure (partial vacuum), causing a sudden release of gases dissolved in the synovial fluid. The time it takes for re-absorption of these gases accounts for the refractory period during which you can’t re-crack the knuckle for some minutes.
As already mentioned in the Wikipedia article in @Rarebear‘s link, there’s a Doctor Donald Unger who cracked the knuckles of his left hand only, leaving the right hand alone as a control, for fifty years! He reported no arthritis in either hand & no difference between the hands. Ref.