Schedule an appointment immediately with principal of the building and request to see a copy of the district's bully policy. Bullying is a serious issue and no child should be fearful in school.
Before the meeting, write down specific events that have occurred recently. If you recall the dates, even better. Otherwise, a list of "who-did-what and when" will do. Make copies for the principal, bus driver, yourself and whoever is the district-level supervisor of transportation.
At the meeting, calmly state that your son is being bullied and that you want it addressed immediately. Then work with the principal to develop a plan to address the situation. Write down what each party agrees to do, including a date that it is to be completed.
After the meeting, write a letter thanking the principal for his/her time and then outline the "plan". Make sure to copy anyone who has a role in the plan and also include the district level administration.
Most schools have a policy regarding violence on the bus and I have worked with principals who take that very seriously & will revoke bus priviledges for an extended period of time. Unfortunately, I have also seen principals who have a less proactive mentality and the events continue to occur.
If you don't get anywhere with the principal, call and request a meeting with the Superintendent.