I do wonder though, do little girls call other little girls ‘boys’ for having short hair?
Me and my one other female friend with short hair were told this in primary in the 90s. She got upset, I just thought people who said it were ridiculous as half their mums had hair like Princess Diana at the time.
At around ages 3-5 children become aware of gender, but they often believe it's interchangeable depending on clothes or hair or even activities or toys thry play with. So they may believe a boy with long hair must be a girl or if a boy puts on a dress he becomes a girl.
At around 6 or 7 they begin to understand that sex is fixed no matter what. But because a girl with short hair or a boy with long hair might be out of their understanding of what is 'normal' they may still make comments. If they continue to make comments after being told that it's ok that's when it becomes bullying imo.
At this age I woukd be wary of labelling it bullying. Some children just won't yet be developmentally mature enough to understand your son is a boy. He will because he has experience and has family members to look up to who are like him. But other kids may not have encountered a long haired boy/man before. My DS likes his hair short but has always known hair is just hair as his DF had long hair whilst I had a Mia Farrow-esque crop.
If kids are commenting bluntly in the way that kids do because they don't understand and are trying to make sense of it then the teacher may be able to speak to the whole class. But if there are kids saying things with the intent to upset your DS then it's bullying. Unfortunately because of their development it's hard to tell at this point if there's intent or not.
My DS is 10 and used to be very feminine in his pursuits. Now he's just 'arty' lol. But he's old enough now to tell people not to be so silly and remind them about gender equality. 