I don't think you need to ask him anything. He needs to be taken to a pediatrician so that he can be examined. Explain what he is doing and ask that he be examined. Pediatricians are obligated by law to report abuse, and you are obligated as his aunt to help him right now. He is showing many signs of abuse. You do not need a 3 year old to vocalize it - he is acting it out. Please do something now because he needs you to help him. Best of luck.
it is to late with the questions you may do more damage than good grt him to a doctor now for his sake lots luck jo
like the other posters said...he needs to be taken to his doctor for an examination. At 3 yrs. old, he may not be able to verbalize what, if anything, happened. Furthermore, if someone is abusing him, it's highly likely that the abuser would have threatened him or somehow manipulated him into not telling anyone and at 3 yrs. old, he may not have had the "good touch, bad touch" talk yet.
Also, does your dad know he's living with the man that abused you as a child? Have you spoken to him about this? Does your nephew also live with your dad, his wife, and your abuser, or has regular contact with your abuser?
Sorry you're going though this.