I had a horrible time with this on my Stamina DK, but not as much with my Magicka Templar. Have not done it with a NB, though. I am still fairly green, so I don't know if someone more experienced has a better approach.
For me, I tried to focus just on one, and let the NPC party keep the other one occupied. Whenever I had both of their attention, I would drop back, and just do ranged attacks on one and/or avoiding until the other one resumed going back to the NPC party. The enemy logic seems to be consistent in the game, in that the enemies seem to gravitate to where it is getting the most damage from. You will do considerably more damage than the NPCs will, so it is really easy to get them both coming at you.
If I am remembering correctly, there are also some other Dremora that come through at the same time, right? Take care of those first so that the NPCs can keep the attention of one of the Atronachs, and so they are not just doing random attacks on whatever is closest. Even then, it is still not easy - or was not for me, at least. I had used a blue recipe (for Health and Magicka), slotted my magicka potions, and used a drain magicka poison, as I had to mix in a healing ability that I normally didn't have in my rotation.