UPDATE
The previously mentioned methods have been patched. If you return to the Supply Point you will now be notified that you need to “Proceed to Ngata”. Once back on the roof, it will again tell you to “Eliminate Ngata” and his health will be fully restored.
On Legendary, with the amount of secondary forces and the nearly insta-kill beam, this boss is woeful unbalanced.
NEW SOLUTION
Similar to the previous solutions, but tweaked so that you do not have to return down to the Supply Point.
NOTE: My agent is Level 5 in explosives. This likely had an impact in damage per shot, so please be aware.
LOADOUT: Decimator, Jackhammer (NOT the Quackhammer, not functionally the same), and Anubis. I had no success with Arc or Incendiary Grenades and did not use them in my successful attempt.
METHOD: From the Supply Point on top of Ngata’s tower, just before the wind tunnel that will push you into the boss battle, climb directly up the incline. If you have double jump, you’ll be able to do it in a straight line from the Supply Point. If not, go to either side of the building and use the edges to climb up, aiming again directly forward from the Supply Point following the tunnel. After a single tier change on the roof, cut to the middle and notice a large open section and look down, you’ll see Ngata.
Lock on, take your time, and don’t fall down. If somehow you are under Explosive 5 and you burn through all three weapons (I had about 46 rounds left in the Anubis, my last gun), you can at least drop down, get some ammo and hit him with everything you’ve got and still be better off than as originally designed.
Good luck! Hope this helps!