Yes, it is, particularly in the sort of conflict we are now engaged in.
So long as we know that the people we are targeting are actively engaged in trying to kill Americans, there is ample moral justification for killing them. We would have no qualms about killing individual military officers in a war. Killing the enemy's highest officers would make a lot of sense because it would degrade their ability to conduct the war against us. If we accept that we are at war with Al-Qaeda, killing their leaders is morally acceptable even if they do not wear uniforms and are not on a traditional battlefield.