Wait, are we talking about the mainline Tom Clancy series or the spin-offs co-written with other authors? The chronology gets muddied because some books are set before 'Dead or Alive' but were published later. For a pure Jack Jr. timeline, start with the prequel elements in 'Locked On' that establish his recruitment, then proceed with the order I've seen on fan wikis. Honestly, I usually just read them in publication order and mentally rearrange the flashbacks.
Why does everyone forget the short stories? They're not full novels, but 'Tom Clancy's Op-Center: Scorched Earth' features Jr. and fits in the timeline. For the novels alone, stick to publication order after 2010. The continuity between authors like Mike Maden, Marc Cameron, and Grant Blackwood is maintained pretty well, with each book referencing the last. 'Command Authority' directly sets up 'Full Force and Effect', for example. It's a military thriller series, not 'Dark Souls', but the timeline has consequences.
If you're listing every book in internal chronological order, Junior's first major appearance is novel #11, 'The Teeth of the Tiger', coming after 'Red Rabbit' and before 'Dead or Alive'. But that's misleading because many of the books before that feature him as a child or teenager. His birth happens around the time of 'Patriot Games'. So he's present throughout much of the timeline, but as a passive character. His active, protagonist role begins two-thirds of the way through the overall book sequence. He fits as a late-blooming main character in a long-running family saga.