Vader does have better TK feats than Windu, but I'm not so sure Vader is powerful enough to directly overwhelm Windu with the force even if Windu is not amped by vaapad.
Also @Han, I think it was Palpatine's own inner darkness along with Windu's inner darkness that completed vaapad's superconductive loop, not Palpatine's dark side energy. Otherwise it wouldn't make sense, because vaapad was said to use dark emotions as a weapon of light without using the dark side. And if Windu was using Palpatine's dark side energy then he would be using the dark side, which contradicts the whole point of vaapad, unless he fountains the dark side enery back out in the form of light side energy.
Either way, Windu wouldn't receive the same amp against Vader that he did against Palpatine, as Vader is not as powerful as Palpatine nor is he as dark as Palpatine.