While I own neither, of the two choices, based on much on-line reading and comparing, the 100-400mm would be my pick. I chose the 400mm 5.6L, and love the light weight, compared to some heavier telephoto zoom lenses I have handled. Some reviewers have written that the 400mm 5.6L focuses faster than its 100-400mm zoom counterpart. Mine does focus right quickly!
Canon 7D2/7D/5D/40D/1D2N/M3; Nikon F6/D700/FM3A/1Dx/Coolpix A; Canon 40mm 2.8 STM, 135L, 50L, 35L, 50mm 1.8 I, 100mm 2.8L Macro, 10-22mm EF-S, 400mm 5.6L, 16-35mm 2.8L II; Nikkor 50mm 1.2 AI-S, 50mm 1.4G, 50mm 1.8D, 16mm 2.8D Fisheye, 180mm 2.8D, 100-300mm 5.6 AI-S, 45mm 2.8 AI-P, 14-24mm 2.8G, 24-70mm 2.8G, Micro-Nikkor 60/2.8G; Voigtlander 90mm f/3.5 SL II, Zeiss ZF.2 2/135 APO