Finding standout stories focused solely on male ninja in 'Naruto' fandom takes some digging, because a lot of the popular stuff inevitably pairs guys off romantically. If you're after the platonic dynamics, the deep friendships and rivalries, that's a different vibe. I've always been drawn to fics that explore the foundation teams, like Team 7 pre-fallout, or the older generation like the Sannin.
One that stuck with me is 'Yet, Again' by esama on AO3, though it's more of a time-loop saga. It's primarily Naruto and Kakashi, with Sasuke and others woven in, but the core is that mentor-student bond strained through countless repetitions. The character work on male fragility and resilience, without romance, is pretty sharp. Another angle is found-family stuff centered on the Akatsuki, maybe 'Hear the Silence' where it's a non-Uchiha OC navigating that world—lots of male interplay, but the focus is on survival and ideology, not shipping.
Honestly, my bookmark list for gen fics is mostly these slower, team-oriented pieces. You have to filter for 'Gen' or 'No Pairing' tags rigorously, and even then, the best aren't always the most kudosed.