I think "are you saying" and "do you mean" are used equally. Both are very natural. Both are used to clarify when someone is being too roundabout in what they are telling you.. "Are you saying that you don't want to date her anymore?" "Do you mean that you lost all the money?" "Are you saying you don't need any help?" "Are you suggesting" is a bit different. Usually the tone is somewhat angry. It is more confrontational. And I think it is used less often, in general. "Are you suggesting that I should apologize to you?" "Are you suggesting that it's her fault that you hit her car?" "Are you suggesting that I should leave?"