This... is interesting. Wellington won Waterloo, and was basically responsible for keeping Spain and Portugal out of French hands. Napoleon conquered all of Europe, minus England, Russia (barely), and Spain.
Wellington had the aid of Spanish guerrillas when fighting the Peninsular war, and for most of the campaign Napoleon was not there. He fought Napoleon's marshals and won consistently. While the French marshals were not on par with the Emperor himself, they were on the whole quite good, and beating them is surely and accomplishment in and of itself.
Napoleon delivered stunning victories against numerically superior opponents on many occasions (Austerlitz anyone?) and made some brilliant strategic moves that caught the anti-French alliance off-guard. His biggest blunder was probably Spain, as in sucked men and effort into a virtual black hole for the entirety of his campaign. Russia was also a bad move, but he recovered and fought back for two more years against more nations than he had previously faced at once and with inferior troops (compared to the men that had won victories like Austerlitz, Jena, and Friedland; not necessarily compared to his enemies).
Waterloo is, to my knowledge, the only time Napoleon and Wellington faced off directly. Napoleon had just come back from exile. His army was not up to the standard of the Grand Armee that died in Russia. However, they still made a good showing. On the other hand, many of the Old Guard were recalled veterans, and they broke in the final charge. Wellington won partially through his choice of ground. However, there were many other factors, including British discipline in delivering volleys even as the vaunted Imperial Guard approached and the timely arrival of Prussian reinforcements (which were able to enter battle because Grouchy did not press them hard enough). Had Napoleon dispatched a more aggressive commander, the Prussians would have been kept off balance and probably been unable to reinforce Wellington, at which point the rest of the French army could have overwhelmed the English.
All in all, it's a tough match. Tactically, I give the edge to Napoleon. Strategically, I would do the same--this in no way belittles Wellington's conduct in the Peninsular war, but Napoleon kept men supplied very far from home and fought a war that literally encompassed all of Europe before mechanization or long-distance communication.
Wellington was also a brilliant general, but he is up against arguably the best in history.