What kinds of meds are these? Are these ADHD meds or does he have a life-threatening illness that requires medication?
If communicating your frustration with your ex does not work, you should enlist your child's teacher or school counselor for help. Have them document what your son is like when he comes from your house (meds) vs. when he comes from his dad's house (no meds). Is his behavior drastically different? Does he act inappropriately? Does he get in trouble more often? Have them document 2-3 weeks' worth of information.
I'd also have your son's pediatrician write a letter stating your son must take his medicine for X, Y, Z reasons.
Once you have all this together, file with the court. Ideally, the judge would order your son's father to give him his medication or he will lose some/all school overnights.
Ultimately, you need to decide is this an issue you're willing to 'die' for or are you making a mountain out of a molehill? Will the angst and anger from your ex be worth the trouble? Is being non-medicated truly life-altering for your son? If so, go for it both barrels blazin'.
Good luck.