I recall reading about his opinion on the matter in one of his books. He lists Israel as a possible suspect saying "Sharon is capable of anything" but then dismisses Israel and claims that Pakistan is the likely culprit. I forget the reason why and I'm too lazy to go look it up. It's a bizarre answer since I don't know what Pakistan had to gain with the attacks, and the ISI is but a bastard stepchild of the CIA with latter in control of the former. I'm not sure why Vidal, a man who is not ignorant of how the world and his country of birth operates, would suggest such a thing.
I have to agree in a certain way what he says about Bush, Cheney and Rumsfeld. Clearly they're either too stupid, arrogant or, more likely, both to have initiated the whole thing. Heck all 3 have pretty much admitted their foreknowledge of the attack on one occasion or the other (Rumsfeld was so happy he was bragging about it a couple of hours before the pentagon got hit) so the 3 stooges would most likely not be the ones behind the atrocity.