How can Gon be so tough physically when he’s just a child? Gon is shown too tough for his age.
In the case of Killua, it is understandable as Killua has undergone a lot of physical torture but in case of Gon it doesn't make much sense or is there a reason behind it?
It may be to highlight the fact that he grew up in the mountains where everything he did was a form of training he did unknowingly. This could explain his insane stamina, speed  and perception of the environment, all before he learned to open the gate, or learn nen.

Other that that, I guess you could say it's some genetic benefit?  Because his father was the only other person in the entire island who single-handedly caught the giant fish, and at the age of 7 no less! Besides it may also be the quirk of someone with enhancement type nen.