There's a sort of jerky rumble from Stone, which after a moment might translate as laughter, when Alfredo jumps like that. It was kinda funny.

A year on this ship has acquainted Stone with some more human mannerisms and gestures, so in lieu of trying to speak and upsetting everyone in hearing radius, in answer to the question he unfolds his arms and gives Alfredo a thumbs up. He's doing great, kiddo, he feels like he can finally breathe again.