What type of story is this? Is the emphasis placed on character, plot, setting or theme?
All the aspects you name are important, in The Adventures of Tom Sawyer and in any other work of literature. You could probably make an argument for each of those aspects as being the most important and most emphasized part of the story.
I would suggest that the novel is, first and foremost, about the character of Tom Sawyer. The settings of the different scenes in the story revolve around the adventures and misadventures in which Tom and his friends engage. The plot of the novel traces his actions and reactions, his attitudes and thoughts as he encounters various people and situations. Themes of imagination, friendship, adventure and curiosity are presented from Tom's viewpoint and others who are interacting with Tom's character.