I misread this at first (I think). For the meaning that I think you intend, it would be clearer to write "You are in/on call-waiting". This would help make it clearer that you are not "on call" and also "waiting".
I don't think there is a single correct answer to this. If the speaker visualises "call waiting" as a queue, then it would be "in". If the speaker is modelling the expression on