Well, after Naruto asks if they've been chased since dawn Jin can just sigh, look tired, maybe rub his eyes, and say something like "It's been a long day."
The implication would be, yeah, it was a long chase, I'm tired, I used my eyes a lot. I'd assume that Naruto has enough experience with Sasuke and Neji to get that using his bloodline a lot would exhaust him so the eye rubbing should clue him in, especially if Jin is notably younger. (How old are Jin, Beni, and Kigane?)