Welcome to elementary school - kids are still learning how to act in groups, sometimes they do the wrong thing. Boys are just as bad as girls, except that boys tend to get over it faster and be friends again sooner. One of my complaints with schools today is that they emphasize how everyone should be included and no one left out, we're all one happy family, etc etc etc. That's not true or realistic. There WILL be people in life who won't like your kid, and there will be people they don't like. We need to equip them with the skills to be kind, but not force them to be 'friends'. Your son will be better served by you teaching him how to fight his own battles then by fighting them for him. If he has problems with this boy teach him to stay away from him or stand up to him.
I would not talk to the other mother. The kids are two grades apart, the amount of contact they will have should be minimal. The best it could do is make you feel better, the worst is that she punishes her son and he retaliates against yours. I would let it go.
By the way, you only know one side. There is a little girl that I know thinks my daughter is mean. She is 2 years younger and pestered my daughter horribly (their brothers were on the same sports team) to the point that my daughter didn't want to go to the games because this little girl would be there. The parents were clueless, she was occupied so they were happy. I had to tell dd to nicely explain to the little girl that she didn't want to play. I'm sure the situation from their point of view looked like my dd was being mean, but she wasn't, she just didn't want to be this kid's friend - and that's ok.