I voted for Season Five. I'm rather surprised more people haven't. I thought it contained some of the very best episodes, Drone and Timeless being the most notable of them. I thought those were classic. And then you had other great hours like In the Flesh, Counterpoint, Latent Image, Dark Frontier, Bliss, Bride of Chaotica, Thirty Days, Relativity, Someone to Watch Over Me (which was very lovely), Equinox. There were one or two really weak episodes (The Disease comes to mind), but ... that gets my vote.
Season Four would be my runner-up. I think, in terms of continuity and ongoing story, Season Two really tried to do the most. They had so many elements running throughout that season (Ensign Wildman's pregnancy, Seska, Suder, alien species hearing rumors of how Voyager was a menace, just lots of plot threads that made it seem like they were really alone and in potential danger). I wish they had kept up that kind of storytelling style. But Season Two also had some weak stand-alones, so ...
... I do think Four and Five, the middle years, were the peak of Voyager, and I have a fondness for Season Five, especially. Though I enjoy all the seasons.