Well, that sheds a totally different light on the subject! She has less familial relationship by far than you do!! My goodness, that means the father (your brother) has had primary custody of these children all that time! I have a better understanding of the situation now! That sister-in-law issue was my only concern. I thought she might be the mother! Even if she was that didn't mean she was the best custodian for the children, only that she does have leverage. However if Mommy is in jail, well that erases that issue.
Now, thank-you for clarifying that. My only advice at this time is...when you have contact with the case worker or the guardian ad litem be as non-confrontational as possible while still being direct. Tough, I know. You want to stay in their good graces. However, they both have superiors. If you feel at any time that you are not being treated fairly, document and go above their heads.
As a matter of fact, go back as far as you can and document anything that is relevant to this situation. By that I mean write down what happened in your own words and sign in and have a witness that is not related to you sign it. If possible someone who witnessed the exchange, but not necessarily. If someone else witnessed the situation or the conversation, have them write their take on the situation. Record conversations, if possible. Don't let anyone know that you are doing that if possible. It will not be admissable in court, but it can be transcribed and notarized. And will hold weight with the authorities involved. The case worker and the guardian ad litem. Also your attorney and his attorney would be very interested in those documents.
You said your brother has prior charges against him. Has he been convicted of anything? If he has...YEEHAW!  That is admissable during the sentencing portion of the trial. As far as custody, get affadavits from the people who are witnesses in those situations. And if the documents are available to you as pending charges or convictions get copies of those. Again, I don't think they will be admissable  in court, but the case worker and guardian ad litem could be influenced by them. Actually, in Family Court, any abuse charges or convictions could be admissable. I don't know. That isn't a criminal situation.
Get a good family court attorney. I repeat, make sure your attorney has family court experience. Check out also the situation in your local family court pro bono availability. If the father hasn't yet applied for pro bono representation, you can. I think. Pro bono means you don't pay.
Now you mentioned that your aunt is helping you. If you have choices on legal representation, then weigh that out.
Once again my thoughts and prayers are with you. I know I have been wordy, but you did ask!! 
PLEASE... report back.