There is no notable difference between "Are you done with your homework?" and "Did you finish your homework?". Both of them are natural in regular conversation, and the answer you would get in response would be the same. :) ((This was not your question, but "above 2 sentence s which one is better?" would be better as "Of the two sentences, which one is better?"))

No. 1 is more American than no. 2, but they both have the same meaning, and sound natural. In UK English you might say ‘did you do your homework yet?’ or ‘have you done your homework?’. To me the phrase ‘are you done with...’ is a more typically American English phrase.