“I was told by one witness, an Air Force enlisted - senior enlisted man, that
he was outside when it occurred. He said that he saw a helicopter circle the
building. He said it appeared to be a U.S. military helicopter, and that it
disappeared behind the building where the helicopter landing zone is -
excuse me - and he then saw fireball go into the sky.

It's a very tense situation obviously, but initial reports from witnesses
indicate that there was in fact a helicopter circling the building, contrary
to what the AP reported, according to the witnesses I've spoken to anyway,
and that this helicopter disappeared behind the building, and that there was
then an explosion.”

Reports of helicopter crashing into Pentagon

 » NEWSFLASH
2:47:43 PM
There are reports that a helicopter has crashed into the Pentagon.
An eyewitness said that they saw the helicopter circle the building and
after it disappeared behind it, an explosion occurred.

(Electrical Contractor Jack) Singleton says worker (Mickey) Bell's memory of
the event is still somewhat clouded. "All that he remembers is that he heard
a loud noise. He thought it was a helicopter coming in to the heliport
behind him. The next thing he remembers is picking himself up off the ground
and seeing the fire and the explosions in front of him," adds Singleton.

http://www.construction.com/NewsCenter/Headlines/DB/20011015h.asp

These photos were taken from the Sheraton Hotel after the crash.   In an email the photographer identified the helicopter as a military helicopter. The helicopter rapidly exited the Pentagon airspace obviously not there for good deeds. The early smoke development corroborates the time:

About 10 minutes ago, there was a white jet circling overhead. Now, you generally don't see planes in the area over the White House. That is restricted air space. No reason to believe that this jet was there for any nefarious purposes, but the Secret Service was very concerned, pointing up at the jet in the sky. It is out of sight now, best we can tell. They've evacuated the entire White House staff and the old executive office, as well as some townhouses that are government offices.

About a half hour ago, the Capitol building itself was evacuated. It was a little bit chaotic. Everyone was running out of the building. People ran a couple of blocks away. Now have been pushed back by security. We're within two blocks of the Capitol. I did see a plane, about a half hour ago, circling over the Capitol. Now whether that may have been a Air Force plane, it's unclear. But that seemed to be the reason, according to security guards that I talked with, towards the evacuation of the Capitol.