Most of the ones that jumped straight into my head have already come up, but I did think of some more:
- Tales from the Loop (and its sequel, Things from the Flood) are both about kids in a slightly more technologically advanced version of the 80's (for TftL) and 90's (TftF), so that could have bits in school. Both have excellent adventures included too!
- Bubblegumshoe! It's about school-aged detectives
- Not 100% if I'm right about this one, but I think the game Unmasked (for the Cypher System) is another that has teen protagonists.