I was going to say that my impression was that it didn't really come together until season 3 or 4, but I just looked over an episode guide and there's some really great, classic stuff in season 2, although there are a few duds too. Ditto for season 3. I'd forgotten how many big storylines and seminal events happened that early in the series.
For that matter, I think you could say the show more or less found its voice midway through season 1. The pilot and episode 2 are pretty good, but the next two after that -- "Emancipation" and "The Broca Divide" -- are pretty awful. Then there's a run of several mediocre ones, but by around midseason there are some more solid episodes, and while the rest of the season is mixed, there are some pretty good ones in there.