Who are the "three mockingbirds" in this story?
Atticus says that it's a "sin to kill a mockingbird" Atticus uses the mockingbird as a metaphor to represent innocence. There are 3 episodes in the story where Scout uses the phrases "to kill a mockingbird" and with each incident she displays a more complete understanding of the relationship between prejudice (or senseless hatred) and the sin involved in harming something or someone who does you no harm.
There are, as you stated, three metaphorical "mockingbirds" in this story: Tom Robinson, Boo Radley, and, although to a lesser degree, Dolphus Raymond.
Tom Robinson is a "mockingbird" because he is a harmless and gentle soul, wrongfully accused by the society around him of a crime he did not commit. In all reality, he is a kind and simple character, and the accusations hurled at him are much like stones or projectiles launched at the "mockingbird" Atticus spoke of.
Boo Radley, whose real name is Arthur, has community rumors spread about him, despite a severe lack of any real grounds for such gossip. Because he keeps to himself, stays mainly inside the Radley house, and has a certain air of mystery to those around him, he is alienated from the rest of Maycomb society, and is a reclusive enigma to others.
Lastly, Dolphus Raymond, who everyone thinks is the town drunk, actually only drinks sodapop from his brown-bagged bottle, and because he loiters about town and acts unusually (according to Maycomb standards, that is), he also is castigated and considered an outcast. The words that people use in reference to him are hurtful, which makes him another sacrificial mockingbird in this story.
The lesson here is that people should not prematurely judge others based solely on outward appearances, a theme that runs through the entirety of Harper Lee's classic about racial prejudice, fitting in, and southern life during the depression era.