I've noticed Bamford's politics in radio interviews of him. I think you're right that he's a leftist, but I don't think that vitiates the quality of his history. He does appear to have gotten most of his facts on the Liberty from sources who were in a position to know.
On his explanation for the Israelis' reason for attacking the Liberty, I think he presents that as his own explanation, and that that can be separated from the facts of his narrative. I think he can be wrong about the first without being wrong about the second (on the facts, what he says is consistent with what other authors say.) I will have to check what you say about the chronology, but, as I said above, my inclination is to believe that what the Israelis wanted to keep hidden was their military plans about future actions in the war, not war crimes in Egypt -- as Bamford claims.
It would be nice if Bamford were to look at why the CIA ordered the Liberty into a war zone in contravention to Naval orders.
It would have been the NSA that did that, not the CIA, but Bamford says that it was, unusually, the Joint Chiefs of Staff that ordered the ship in in the first place. I assume he is correct about that. My recollection is that Bamford does say that the Pentagon tried to order the ship back out of the war zone, but that there was a snafu in transmitting the orders. I suppose it's possible that people are lying about that, that the mistransmissions were deliberate, and that people in the Pentagon were trying to keep the Liberty in place. I find it hard to see how the CIA could have been involved.
In any case, whatever was going on, the Liberty may have been in a war zone, but it was in international waters. It was indeed collecting signals intelligence, but to do so in international waters -- war zone or not -- was perfectly legal, under international law. Israel had no right to attack her, even if somebody was disobeying presidential or other internal U.S. orders. The sailors, who were obeying all the orders they knew about, did not deserve to die.