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Who would win this fight?

I would answer this, but I'm honestly not familiar with the term NJO. Chalk it up to lack of research.

NJO is New Jedi Order (about twenty years after Return of the Jedi)

NJO = New Jedi Order.
And this one is stupid, 'cause they'd never fight each other.
Unless you mean sparring....

Fine, I'll make the question "who's more powerful?"

No, I'm just saying, it isn't ver realistic, (even for SW). I mean, they'd have no reason to fight each other.
But I think NJO Luke would win....

Hm. Honestly couldn't tell you. But I think since Yoda was the master, and was a bajillion years old and could still kick it with Dooku, he'd probably whoop Skywalker around and still have time to raid his lunchbox afterwards.

Yoda was wise, powerful, but old.
Luke is younger, stronger, and considering his father's father was the force, you can argue Luke has a stronger connection to the force.
So I would say Luke, but they would only be sparring.

Now if it was like a crazy darkside Yoda...