Clearly, your son is asking for help, and something has to be done or the possibility exists that he will sprial into such behaviors as drugs, alcohol, or even crime to get somebodies attention. Now is the time. He needs to come live with you, however you can make it happen.
Your daughter may be "alright for now" but your son is not. If you can not reach an agreeable solution with his father. (step mom has no legal ground, your discussions need only be with the father) then a mediator (state provided) is the next step.
I would schedule a meeting with the father, a school counselor, the boy & you.
If no resolution:
Then contact a state mediator. What you decide in their office is legally binding. They will also have the courage to tell you husband that he is being unreasonable, where the school counselor may not. If this does not bring a solution:
You may need a lawyer, & an child study..parenting evaluation.... I can't remember what they are called.
You said moving 50 miles is not an option, it may become necessary. There is value in keeping the kids in the same school, it will provide consistency, & as they grow their peers become more important (in their minds) than parents. It may be a huge sacrifice for you, but you only get one shot at raising the kids, and in this case your son is asking for PROTECTION. However it puts all of you closer to the step mom, which may have a detrimental impact, but being in the same town obviously eases the visitation issue.
Splitting them up may not be your husbands choice, but when it comes to a kids survival, he is putting his desire over the kids NEED. Your son is the real one caught in the trap. You do have the power to make a change, even if it's not comfortable. There came a time that my son declined visitation on account of the step mom. Loves his dad, but not when he's with her. "She runs the show, & hates men" according to my son. So my daughter is fine with her, but the son is not. He sees his dad only now, once a week, then the family on special occasions, birthdays.
So moving your son in with you, may take state intervention, if dad has legal custody. The step mom you said is the one who makes it miserable. Somebody needs to tell her to back off, & perhaps, in a nice way to "shut up." This may also take state intervention. Don't be afraid of her, your son is at risk, and he needs you to take action.
I can recommend lawyers, and counselors if you are in the Portland area.
This is not an easy road, Co parenting rarely is. Obviously there are REASONS the marriage didn't work, and likely the same reasons you are having difficulty with this now.
May God bless you, and come along side you, & provide a way for you.