Simply put: because each of their targets has committed some form of crime, while remaining out of reach of ordinary investigative methods. Phantom Thieves is merely what they call themselves. They claim to steal not objects, but hearts...or rather, their target's motivations to perform evil acts. Shortly after they send their calling card, their target has something of a change of heart regarding their actions and publicly confesses to them.

They even caused a yakuza don to turn himself in with a full confession, after he had successfully eluded our attempts to locate him for quite some time. Seeing as the results of their actions have uniformly been for the betterment of society and the safety of its citizens, that is why I believe their motives to belong to the realm of justice.