Where does “नैन” come from?

नैन (Hindi) comes from Sanskrit नयन, from Sanskrit नी, from Proto-Indo-European neyH- — to lead.

नैन (Hindi): eye

Definitions

Step	Language	Word	Meaning
1	Sanskrit	नयन	eye; leading organ; conducting, guiding,...
2	Sanskrit	नी	to guide, govern, direct
3	Proto-Indo-European	neyH-	to lead

नैन — Etymology, Origin & Word History | Etymology Explorer