Sexism isn't just excluding or discriminating, there is one other vital component: harm. It's like having a girl's bathroom and a boy's bathroom. The girl's bathroom might even have more facilities (tampon machines/disposal). It's not sexist because it doesn't disadvantage either gender, it's simply discriminating for a perfectly legitimate reason.
Unless someone can show that this school will somehow harm boys then it isn't sexist.
It may not be sexist, but it might be illegal. Title IX, explicitly prohibits excluding students from participation in or the benefits of ANY education program or activity receiving federal financial assistance.
The most issue addressed by Title IX is spending money supporting a football and wrestling teams (which is predominately boys). Title IX pretty much says if you spend that money there, you have to spend an *equivalent* amount of money providing sports opportunities for girl on the grounds that in a zero-sum game of money, girls are *harmed* because you spent that money on something that only benefits boys.
Of course things cannot be totally equal in every situation, so there is a 3-part test to be evaluated
1. percentages of M/F students in an activity (e.g., like sports) that accepts federal funds are about the same as the student population (this is the easiest way to show compliance)
2. equal opportunity exists for M/F students in that activity (very hard to show if you exclude 1 gender), OR
3. school is fully providing opportunities that meet the interests and abilities of M/F students
I suspect where this whole things falls downs is #3. By excluding boys from this STEM program and only providing a Language Arts option for boys if there is a significant number interested in STEM (I'm guessing, there are quite a few of them), I don't think this will survive an equitable legal challenge (imagine if it were the reverse). Having said that, legal challenges today are intertwined with politics and judicial activism, so it's hard to say what the result actual legal challenge result might be.