I haven't seen Season 4 yet. I'm waiting for when the R1 DVDs come out (on my birthday! Yay!).
As for the other 3:
1st place: Season 2.
It's just chock full of episodes that really kick ass, like "School Reunion," "The Girl in the Fireplace," "Rise of the Cybermen," "The Age of Steel," "The Impossible Planet," "The Satan Pit," "Army of Ghosts," & "Doomsday." David Tennant is my favorite Doctor and just comes roaring out of the gate. Mickey becomes a companion! (I simply skip over "Love & Monsters" & "Fear Her" when watching it on DVD.)
2nd place: Season 1.
The 9th Doctor/Rose chemistry is very strong. "Dalek" actually made the Daleks scary again. There's also some very strong character stuff in "End of the World," "Aliens of London," "Father's Day," "The Doctor Dances," "Boom Town," & "The Parting of the Ways." I liked the reality show send-ups in "Bad Wolf." Really, there's hardly a bad episode of the bunch.
3rd place: Season 3.
Honestly, I like Martha a lot. I just didn't like her relationship with the Doctor. I didn't like that the Doctor remained so hung up on Rose for so much of the season. Martha's mother is like a less funny rehash of Rose's mother. Mostly, the episodes in Season 3 just felt tired. The only ones that really had anything interesting to say were "Human Nature," "The Family of Blood," & "Blink." The BBC could trash the rest of the season 1970s style and it wouldn't be any huge loss.
P.S. I suspect that when I actually see Season 4, it will at least be better than Season 3. I can't imagine another season of such mediocrity.