Another possibility is Harry Potter himself. This would be a very different take on their relationship. In some fanfiction, the strong bond between Hermione and Harry could be taken to a new level. Maybe in a situation where they are the last hope for the wizarding world, they conceive a child in secret to carry on some special magic or power that could save the wizarding community.
Another option could be a new character. A mysterious and powerful ninja from another village who Fem Naruto met during a diplomatic mission. They had a short - lived romance, and he doesn't even know about the child. This would add an element of mystery and the potential for the father to show up later in the story.
It could be Ron. Maybe they had a falling out or some complicated situation that led to Hermione keeping the baby a secret from him.
Perhaps it could be a new character. A mysterious wizard who comes into Hermione's life, and they fall in love and have a child. This would add an element of newness and mystery to the fanfiction, as the readers would get to learn about this new character and his relationship with Hermione.
Ron could be the father. Given their relationship in the original series, it would be a natural choice. They could have gotten married and had a son. Ron's laid - back nature might contrast with Hermione's more serious side when it comes to parenting their son.
It could be Edward. Since they had a deep connection in the original story, it would make sense for him to be the father in the fanfiction.
It could be a powerful wizard who has been in hiding all this time. Maybe someone with a dark past that the author wants to explore.
It could be a jealous wizard who was once in love with Hermione. Discovering she has a child with Fred, this wizard might seek to harm the child out of spite. He could use dark magic to try and kidnap the child or cause trouble for the family.
Another option is that the father could be Harry, but in a very different and alternative take on the story. Maybe there was a situation where they got closer than friends during a difficult time and it led to the baby. However, this would be a very radical departure from the original relationships in the series.
It could be Ginny. Even though in the original story they are married and have kids in a more normal way, in fanfiction, there could be a twist where their relationship had a secret earlier on and she is the mother of the secret child.
It could be a random villager that Naruto met during one of his travels. Maybe she was from a small village that Naruto helped protect, and they had a brief encounter that led to the child.