The most likely phrasings would be
I saw a ball thrown from the window.
I saw a ball thrown out of the window.
I saw a ball dropped from the window.
Since those actions (drop,throw) would lead to such an event occurring. If you really didn't see how it started, and only know that it's "falling", can you even be sure it came from the window? Maybe it's falling from the roof instead.
I saw a ball roll (or fall) off the window ledge.
with that same image in mind, this makes sense:
I saw the ball fall from the window (ledge).
Finally, if none of those options work, your original sentences with "from" or "out of" are probably acceptable.