I wouldn't call it marketed at teens/young adult audience, but this is Richard Paul Russo's Ship of Fools (titled Unto Leviathan in some markets).
It's a SF horror novel set on the Argonos, a generation ship that's been voyaging for a very long time that is slowly failing. The inhabitants have long since forgotten their original mission and are now just looking for a planet to settle. The viewpoint character is Bartolomeo, a cripple (and I believe, a dwarf?).
The ship detects a radio signal from a planet that appears habitable, so it heads there... only to find nothing but ruins and bones; though it was a human colony, something unknown has killed everyone on the planet, which they name Antioch. Eventually they discover
a vast room [in which] there are contained, on hooks and in chains, an unimaginable number of mutilated human skeletons, including a number of children and infants.
The Argonos departs, and next finds a giant ship, bigger than it, seemingly empty at first, that was apparently the target of that earlier signal, but then
a solitary old woman is found in a compartment of the ship which, unlike the rest of the explored sections, inexplicably has Earth-like gravity and air breathable to humans. At first, the old woman is unable to understand the languages used to communicate with her and speaks only in gibberish. She eventually begins to communicate with scientists in English.
Eventually she turns out to be something different, and is ejected into space.
