McEwen completed the leg from Huy, Belgium, to Saint-Quentin, France, in four hours, 59 minutes and 50 seconds. But he was sixth overall despite the strong showing Wednesday and a win in Monday's second stage of the annual cycling competition.
Issac Galvez of Spain was second Wednesday and Boonen was fifth to hold on to the coveted yellow jersey signifying the overall race leader.
George Hincapie of the United States finished 14th but was third overall.
The fifth stage of the Tour will take the riders from Beauvais, France, to Caen. The Tour de France ends July 23 in Paris.