In small, heavy-bottomed pot, arrange chicken breasts in a single layer. Add quartered onions, smashed garlic cloves, bay leaf, salt, peppercorns, and enough water to cover.
Bring to a boil, skimming scum that floats on top. Lower heat, cover, and cook in a barely a simmer for about 10 to 15 minutes or until thermometer inserted in the thickest part of chicken reads 165 F.
With a slotted spoon, remove chicken from pot and allow to cool to touch. Coarsely shred chicken and keep warm.
Strain liquid using a fine mesh sieve. Discard bay leaf and peppercorns. Reserve the softened onions and garlic and 1 cup of the broth.
In a blender, combine chipotle peppers including sauce, tomatoes, the softened onion quarters, garlic, and 1 cup reserved broth.
In a wide pan over medium heat, heat oil. Add onions and cook until softened.
Add pureed chipotle tomato sauce, vinegar, cumin, and oregano. Bring to a simmer for about 2 to 3 minutes.
Add shredded chicken and continue to cook for about 7 to 10 minutes or until heated and sauce is thickened.
Season with salt, if needed. Serve hot.