If I was told to choose my top 3 it'd be: McGann, Tennant and McCoy. They're the Doctor's I return to the most when I'm re-watching old episodes. I like Smith too, but he's the current Doctor so it's kind of hard not to watch his stories
But if I was forced to pick just one, it'd be McGann. He did the impossible, he made his Doctor endearing in a script that was essentially a regeneration story and left him with amnesia through most of it.