I used to work with crime victims as an advocate, so your friend's situation is one that I've heard of over and over from many women. As others recommended, your friend needs to document everything that is occurring with the child's father, AND she needs to call the police anytime she has an encounter (by phone or in person) with this guy that makes her feel afraid, i.e. harassment, stalking, trespassing. If there are police reports on file of this man's harassment, that can eventually help her get supervised visits or even help her end visitation altogether.
A couple of people mentioned that she needs to get a restraining order, but restraining orders don't protect people, they only protect property. What she needs is a protective order, which are usually issued through the district attorney's office. Typically the DA's office will provide them to women who have been seeking assistance from the police department for harassment and/or threats of some sort. She can also have the police issue a criminal trespass which would prevent him from coming near her property, and if he did, he would be arrested.
You are a wonderful friend to seek out help and information for her. A woman in her situation needs tons of support, especially locally, so I would also recommend that she seek assistance/support from the victim advocate in San Antonio. She may not see herself as a victim based on the current circumstances, but based on the information you've shared, she and her children are very much at risk for being hurt by this man. Here's a phone number that she or you could call to help her get connected to more support:
San Antonio Police Department
Victim Advocacy Section
Victim Advocates work closely with the police department and can help women through the hurdles in the legal system.
Best wishes to your friend. I hope she can get the help she needs to protect herself and her family.