That's a great question! I have the AF Nikkor 50mm f/1.4D, and it seems pretty flare-resistant. Perhaps the f/1.8 is even more flare-free. Maybe even better, the AF 60mm Micro-Nikkor f/2.8, or its 55mm f/3.5 variant, since the front element on those lenses is so far recessed. On second thought, any of Nikon's new, Nano-coated lenses should exhibit superior flare-resistance.
I do know that the smaller the glass, the less dispersion, so based on that, the old 55mm f/3.5 Micro-Nikkor may be the winner, with its ultra-tiny, recessed front element.
Internal flare can also be minimized by shooting with a bellows-style matte box attached to the front of your lens. The ones made for the Mamiya RB/RZ67 and 645 medium-format cameras are just large enough to fit some of Nikon's smaller primes. Unfortunately, these accessories are no longer made, and must be purchased used. Lee, and others, make bellows matte boxes for still photography, but tend to be fairly expensive.