Of the modern seasons, I'd go 4, 2, 3, 1.
Season 4: The only episode I'm not really a fan of is "The Fires of Pompeii," everything else is gold.
Season 2: For me, this seasons scores so high due to the chemistry between Tennant and Piper. Together, they really sold the characters and their romance.
Season 3: When it comes to the episodes, this is better than the second season, but I never felt a connection with Martha. And that hurts the season a little.
Season 1: It does a great job bringing the Doctor back, but it could have used more alien worlds and less farting aliens.