For what it's worth here's the basics re Cicale's account of the Cirillo incident:
Around Spring 2004 Dominick Cicale was having renovations done on his real estate office. Cirillo showed up at the office to discuss money owed for the work and Cicale told him to mind his business. Cirillo raised his voice and Cicale slapped him. Cirillo then started toward his vehicle and made a comment about getting a gun. Cicale followed him, held him against the car and started beating him so he couldn't get at any weapons. There was a guy with Cirillo who was still inside the vehicle. He told Cicale there wasn't really a gun inside so he backed off. Both parties left the scene. Almost immediately after they were gone Vincent Basciano Jr. showed up and was questioned by the NYPD who been called to the location and had also just arrived. Cirillo did not hit or threaten Basciano Jr., they weren't there at the same time.
A few hours later Cicale was summoned to meet with Vincent Basciano, Michael Mancuso and an unspecified Genovese member. It was decided since Cirillo didn't actually put his hands on Cicale there was no issue and to let it end there. The Genovese member made a call and Cirillo showed up and apologized to Cicale for his behavior. They shook hands and that was it.
Cirillo was last seen May 9, 2004. Shortly thereafter Cicale met with Basciano and Mancuso. During this meeting Basciano expressed his opinion that the Genovese were taking advantage of the recent situation between Cicale/Cirillo to get rid of Cirillo and have the blame pointed elsewhere. Basciano told Mancuso to meet with one of the Genovese leaders (poss. Lawrence Dentico) and inform them the Bonannos had nothing to do with it. Mancuso and the Genovese met and they told Mancuso they already knew the Bonannos weren't responsible and no further action was taken.
After Cicale was indicted he spent time with Dominick Cirillo at MDC Brooklyn, and Cirillo also told him he knew Cicale had nothing to do with killing his son.
As for who was really responsible there's a lot to go back and forth with. For me, it's hard to believe Cicale would plead guilty on two death penalty eligible murders (Santoro/Pizzolo) yet lie about involvement in a third. Particularly when the victim in question wasn't some kind of innocent civilian. Not to mention Pisciotti, who hated Cicale by the end, also deciding to withhold info.
On the other hand, that's doesn't preclude other Bonannos having some degree of involvement, whether it's Basciano himself having a role (or just advanced knowledge) or Pizzolo being recruited off the record. If so Basciano really went all out with the lie, denying it to everyone up to and including his own boss.
Given what's available to us, I'm leaning toward it being the Genovese who carried it out, with the Bonannos being made a convenient scapegoat. But there's enough conflicting info on the situation to keep at least some of the opposing theories viable. What's really needed is a cooperator from the other side. If it was a Genovese only hit then one or more of the participants are likely still out there. Any one of them could potentially get indicted on serious charges somewhere down the line and decide to flip and clear things up.