Because TSCC starts following the events of Terminator 2, it specifies that John was 15 during those events, and that he celebrated his 16th birthday during the first season finale (What He Beheld).
Regarding Thomas Dekker's age, it is not unusual for actors to play characters who are significantly younger than themselves (for example, Keiko Agana was 27 years old when she began portraying the character of Lane Kim on Gilmore Girls [an 11-year age difference between herself and her character], and Alyson Hannigan and Nicholas Brendan were 23 [Alyson] and 26 [Nicholas] years of age, respectively, at the time they began portraying the characters of Willow Rosenberg and Xander Harris on Buffy the Vampire Slayer [both Willow and Xander were supposed to be 16 at the start of the series, meaning that there was a 7-year age difference between Alyson and her character, and a 10-year age difference between Nicholas and his character]).
John should, technically, still be going to school, but now that they are once again trying to lay low, and given the change in his attitude, he's no longer going consistently.