It can't be Fredo. He never knew it was supposed to be a hit, so he couldn't have been prepared to find them and kill them. He also was too weak and ineffectual. He couldn't even defend his own father when he was shot. And Deanna is screaming about men outside her window, which makes sense if Michael's bodyguards were scouring the property.

There's also no way Anthony did it. He wasn't even sure what his father did for a living at that point. If he was withdrawn in the remainder of the film, it was because of the tensions building between his mother and father and their eventual separation.

There was probably a third person who killed the other two and got away.