Season one had a fun feeling of newness and energy. The season is full of unique character moments (like Neelix and Kes bringing trays of food to the bridge during a crisis). Also, the issues of being stranded in the Delta Quadrant on a ship with limited resources and a crew of renegades are dealt with. I enjoyed many season one episodes, like "Phage", "The Cloud", "Eye of the Needle", "Prime Factors", "State of Flux", "Faces."
However, the show was probably at its best in season five. The production design was slick and the episodes (while mostly stand-alone) were of good quality. "Drone", "Timeless", "Counterpoint", "Dark Frontier", "11:59", "Relativity", "Someone to Watch Over Me", "Bliss", and others were produced in this season and are some of the show's most memorable hours.
I'd go with season five as Voyager's best overall season.
-Aaron