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.”