Sometimes none, but there can be a difference. "Are you at work" usually means "Are you at your place of employment?" "Are you working" usually means "Are you busy with work right now" (maybe work at home, not just at the place of employment). You could be "at work" but not "working" because you are at your place of employment, but you are on a break or at lunch. If you are talking to somebody who might be working on something at home, and you wanted to know if they were busy or free to talk to you, you would say "Are you working?" You would not say "Are you at work" because you know they are at home and not at their place of employment.

Saying "Are you at work?" Is another way of asking, "where are you?" Saying "Are you working?" Is another way of asking, "what are you doing?"

If you are meeting someone for the first time you can ask them "are you working" just like you would ask "are you a student?".