What does he want to major in?
APES is seen as a science class and it’s one of the few classes (with AP Human Geo) that deals with current events/world news issues. While it’s not as rigorous as AP physics, since he’s got all three (bio, chem, physics) plus CS, he’s fine.
Does the school offer Honors Calculus?
If not, he should definitely take math senior year, but AP Stats would be okay.
If he intends to major in STEM, economics, or business, AP Calc AB would be a good choice, but schedule one less class so that he can take tutoring.
He should have English, Math, FL, History/Social science, science, and one class of personal interest. Does he?