FIrst of all, you may have a case for statutory rape. That means that whether your daughter "voluntarily" "consented" to sexual relations with this young man, she doesn't have the power to consent since she is a minor and since he is at least two years older than her, it would be considered statutory rape (rape per the statute covering sex with minors). You can alert the authorities by filing a police report; then the police department would have to refer the matter to the county prosecutor for review and possible charging. But I will tell you, as a former prosecutor, statutory rape is not the type of case most attorneys want to take on because it is seen as a lower level offense and sort of "victimless," unless there is a child molestation situation going on or something of that nature. But you can still try to see if they will take the case.
As for custody, if the baby is born live, the mother and father will have exclusive rights to that, unless you can prove that father is completely unavailable (as in, on a ship in an ocean somewhere) and mother is not competent to raise the child. Despite what appear to be numerous mental illness diagnoses, it still may be hard to convince a judge that she can't parent the infant. You will just have to see how it goes and, if it looks like her caring abilities are inadequate -- that is, drastically below the norm or actually putting the child at danger of imminent harm -- then you may file something with the court asking to step in as "in loco parentis," which means in the role of a parent. Best of luck to all of you!