Yes, all are correct., there are some subtle differences though. The first is a genuine question where you do not know the answer to. The seconds and third show surprise, you *expected* him to be 'up' (out of bed) or 'awake' (not asleep) and are surprised he is not.

"up" means out of bed, you will also hear "is he down yet" which means he out of bed, has dressed (partially?) and is now downstairs (probably looking for breakfast) "awake" means he can still be in bed but is no longer asleep Is v Isn't practically means much the same and even the answer "yes" or "no" will depend a bit on context. Isn't he up yet? Suggest a certain frustration with the person in bed.