His mother could send the howler. In the wizarding world, mothers can be quite fierce when it comes to family reputation and she might be unhappy with Sirius's actions or friends.
It could be Severus Snape. He has a complex relationship with Dumbledore. Maybe Snape discovers some of Dumbledore's plans that he doesn't agree with regarding Harry Potter. He then sends a Howler in a fit of anger to express his disapproval.
Perhaps another student, like Hermione, could send the Howler in a very creative twist in the fanfiction. Maybe she has found out that Draco is planning something malicious against the Gryffindors and uses the Howler as a way to threaten him into stopping.
Hermione could be the sender. If Snape has made some unfair judgment in class against Gryffindor students, Hermione, with her strong sense of justice, might send a howler to him to voice her protest.
His mother is a likely sender. She could be worried about Remus and send a Howler to remind him to take his Wolfsbane Potion regularly or to be more cautious around others. Mothers are often protective, and in the wizarding world, a Howler is a rather forceful way to get your point across.
It could be Professor Snape. He often had a contentious relationship with Harry, and if Harry did something that Snape thought was particularly wrong or against school rules in a way that affected Snape's interests, he might send a Howler.
It could be Dumbledore. He was always one to oppose Voldemort and a howler from him would be a very interesting plot point. He might use it to taunt Voldemort or to try and make him second - guess his actions.
Snape could face some backlash from the Ministry. If they find out that he was involved in getting rid of Umbridge, they might try to find ways to punish him or at least keep a closer eye on him. However, his skills at subterfuge would likely help him avoid any serious consequences.