Nah man, Tom knew about Pentangeli's survival from Fredo, he relayed this news to Mike. Fredo probably told Tom about Questadt too but Tom let Fredo hang on to that and tell it to Mike himself, as it may have gotten him off the hook.
The dialog from the boathouse scene when Michael exclaims, "Pentangeli is alive!" doesn't support your viewpoint:
MICHAEL: What about FREDO? What does he know?
TOM: He says he doesn't know anything -- and I believe him. ROTH well he -- he played this one beautifully.
MICHAEL:I want to talk to FREDO.
Tom found out about Pentangeli's survival from the Senate committee (either the chair or Questadt) because they were required to disclose to him the witness they were about to use against his client (Michael). Fredo probably did tell Tom he knew nothing--then, when he was with Michael, he blurted out that he knew Pentangeli was alive, and that Questadt belonged to Roth. That would have made Tom look like a fool for telling Michael, just a bit earlier, that "He says he doesn't know anything--and I believe him." Not the stuff to ensure warm feelings all around.
