It obviously depends on what you expect the Doctor to be.
A few years ago, I'd have said Baker (Tom, naturally) and been done with it. But that's just a side effect of my age, and his long tenure in the role. I've gone back and watched a lot of old Who as well as the new in recent years and it has changed my perception a bit.
Based on that, Patrick Troughton has ended up my favourite. Followed by Matt Smith, who's essentially emulating a younger version of him. It's a pity so much of Troughton's work is still missing, but the recently uncovered episodes were *excellent*.
I wouldn't go so far as to rate the rest of them. They've all been good in their own ways (even if for Colin Baker, it's been off-screen in the Big Finish plays). Certainly Tom can beat them all for presence and sheer pomposity, but having re-watched all of his stuff in the past few years it's really quite astonishing how bad it is in places and how often Tom just phoned it in. Out of the two most maligned actors in the role, Syl was starting to get into a very good groove just as the series was canned, and Colin proved beyond a doubt in later work that it really was just abominable writing and directing that made his years so shit.
All of that is because I like the idea of the Doctor as a playful alien with a heart of gold. If you think he's better suited as an imperious guardian of good then Pertwee or Tennant will be more your thing.