Flood vs Nids is interesting but I'm ultimately giving it to the Nids since all of their ground forces are reduced to a nutritious gruel in the end and recycled. Not to mention a good portion of the planet's crust.
Also the infection form doesn't instantly infect everything so the Nids would likely just eat them along with everything else on the planet. Plus it's debatable if the individual Nids are setinant enough to even be infected. Finally the Nids can basically redesign each generation in minutes. So they could rewrite themselves to be immune.