What is ironic about Finny's remark that he knows Gene better than anyone else in A Separate Peace by John Knowles?

It is, indeed, ironic that Finny tells Gene in Chapter 11, "I know you better than anybody," because he truly believes that Gene is his loyal friend. Despite what others suspect and know, Finny does not suspect Gene of any jealousy or of having jounced the tree limb, an action which has caused Finny's terrible fall and broken leg--a shocking fact that Finny learns at the end of this chapter.
Finny's statement about Gene's loyalty comes as he listens to Gene, who helps him with Latin. Gene translates Julius Caesar's recounting of his war against the Gauls. It is revealing of Finny's character that he has never believed that Caesar and ancient Rome ever existed, but thinks that tales of Caesar and Rome were merely created to be the "bane and bore of schoolboys." Nor has he believed that a world war exists now. 

"Naturally I don't believe books and I don't believe teachers,...but I do believe--it's important after all for me to believe you. I've got to believe you, at least. I know you better than anybody."

In affirmation of his faith in Gene, after Gene informs Phineas that Leper has "cracked," Finny tells his roommate that he believes him, and he now believes that there really is a war: "If a war can drive somebody crazy, then it's real all right." But, he does admit that at first he doubted Gene's words, thinking that perhaps Gene's imagination became "a little inflamed in Vermont" when he visited Leper. 
This conversation hints at the possibility of doubt in Finny's mind about everything that Gene says.  This doubt is raised later when Brinker and three "cohorts" enter their room and escort Gene and Finny to the Assembly Room for an "inquiry" into what actually happened on the night that Finny's leg was broken.
Still believing in Gene during his questioning by Brinker about their positions that night, Finny turns to Gene, "You were down at the bottom, weren't you?" When Gene lies and says that he was, Brinker then questions Gene. Further, he asks if Leper Lepellier was there at the river, and a voice affirms that he was, and also states that Leper is on campus. Brinker sends the two cohorts after this new witness, and Leper soon enters the room. Leper testifies that he was standing at the bottom of the tree, and he shaded his eyes against the sun so that he could see above him the two boys:

"The two of them looked as black as--as black as death standing up there with this fire burning all around them."

He testifies that he could not make out the boys; they were just "two shapes." Then he says, "The one who moved first shook the other one's balance." But he will not "implicate" himself; he refuses to answer Brinker on specifics. "I know when I have information that might be dangerous."
Shortly after this, Finny rises and interrupts, "I don't care." Frantically, Gene runs to him, but Finny closes his eyes with his face revealing no expression. "I just don't care. Never mind." He then rushes from the room, shouting with emotion, "You get all your facts!...You collect every fact there is in the world!"
Finny's hurried departure is heard as his cane raps along the corridor; then, his tumbling body is heard striking against the marble stairs. Finny has been devastated by the terrible irony of his having believed that Gene is his loyal friend.