They are all good but there could be a difference between “Who do you live with?” and “Who lives with you?” If I am an owner of a house, someone would ask me “Who lives with you?” “My nephew moved in last month. He’s staying with me while he gets his Master’s” If I’m a student in a foreign exchange program, someone would ask me “Who do you live with?” “I’m staying with a nice retired couple who wants to practice their English.”

They all make sense, although "Who lives with you?" seems awkward.

Both of those questions are correct and natural. “Who do you live with” is also correct and natural, and means exactly the same thing as “who lives with you?”