You could also say something like, もう帰国しましたか？ Or just, 帰国しましたか？

I personally would ask （もう）日本に帰ってきました。

If you want to speak Kansai dialect in casual way, then "mou ninon kaette kitan?(↓)" would be fine.

(あなた) 日本に帰っていますか？ (Anata wa) Nihon ni kaette imasu ka? The "Anata wa" is not necessary if you use the sentence in a context that makes it clear that you are asking about the person hearing the question. It's also possible to use the person's name as in "Kumiko-san Nihon ni kaette imasu ka?" but that's more formal than just simply asking "Nihon ni kaette imasu ka?"