Neither seem like natural fighters, but I'd go with Neal.

He's a lot sneakier than Will is. Besides, Hook managed to defeat him with only a single move during the whole Snow Queen's magic mirror, so that loser wouldn't be very hard to beat.

As much as I like Will I must admit that he is really lousy fighter.The man doesn't know how to punch.
Neal on the other hand was pretty handy with a sword & a staff!

Well, to his credit, I'm pretty sure Will was drunk when he confronted Killian, but yeah even sober he's pretty clumsy and uncoordinated compared to Neal. xD

Wiill is the "village idiot" so Neal....