Seeing as how one of a Ninja's main abilities is going invisible (at least till they can turn ethereal), and this annoying little fact of underwater combat:
"Invisibility
An invisible creature displaces water and leaves a visible, body-shaped “bubble” where the water was displaced. The creature still has concealment (20% miss chance), but not total concealment (50% miss chance). "
Perhaps some magic items to negate the outline he would normally leave in the water, so as to be fully invisible, like on land?
An ability in line with krup's could be some unlimited use ability like Jet, as the giant qsuid special quality. That could prove useful.
"Jet (Ex)
A giant squid can jet backward once per round as a full-round action, at a speed of 320 feet. It must move in a straight line, but does not provoke attacks of opportunity while jetting. "
The squid's swim speed is 80, so this is basically just a run action (4x speed) that doesn't provoke attacks of opportunities. I assume the Ninja already ha a swim speed from his race,so he cna already take a run action in water, this would just improve it slightly.