To me: 1 and 3 are the same, but 3 is a more natural and common way to ask it. The progressive aspect in 2 suggests a longer time. You would typically ask that for something that will happen over an extended period. There is therefore an implication in your second question that the homework will take (say) an hour or more to do, and therefore you will expect to get an answer that is a longer period of time, such as 'tomorrow afternoon' or 'friday after dinner'.

When will you do your homework? When are you going to do your homework? This is just future - I think these imply at what pont in the future will you start to do your homework. When will you be doing your homework? This is future continuous - at what point in the future wil you be in the act of doing something here homework.