Depends on how you define "target". I would think that the jetliner that was crashed into the Pentagon was just as much the target as the Pentagon itself, and in fact was responsible for most of the casualties.
Had they flown, say, a cargo plane into the Pentagon rather than a Jetliner then I would agree, but they chose a jetliner, and I think the jetliner was more the target than what they crashed it into.
In any case I agree with the way you put it for the Cole: The group that carried out the attack is clearly at terrorist organization, even if not every one of its attacks is terrorist, and even if ALL their attacks are criminal. Al Qaeda certainly has committed no shortage of acts that are terrorist by ANY definition of the word, such as the repeated attacks on the WTC.