With whom do you live? is the correct one as you should not put a preposition (with in this case) at the end of a sentence. However, this rule is broken all the time, so you will hear the other one more frequently.
In spoken English in the UK people also say: "Who do you live with" ..
Whom is going to die out here soon, I agree,
and that ridiculous "rule" about not ending with a preposition is a rule you'd be better off never even learning - it jsut give you another thing to stress over.