Place onions, garlic cloves, salt and oregano in large stock pot. Add chicken thighs on top.
Add broth and bring to a boil over medium high heat and reduce heat to medium low and simmer for 30 minutes, stirring occasionally.
Remove chicken from pot and set aside. Use a slotted spoon to remove the onions and garlic. Remove broth and reserve.
Add oil and 1 diced onion to the same stock pot. Cook over medium heat until onions begin to soften, about 5 minutes.
Transfer the reserved broth to the pot and over high heat, boil mixture until liquid is reduced to half, about 20 minutes.
Add reserved onions and garlic, tomatoes and chipotle peppers to a food processor. Process for about 5-10 seconds or until smooth.
Add tomato puree mixture to the pot with broth and onions.
Shred or chop chicken and add to the same pot.
Cook for 20 minutes over medium high, stirring occasionally as sauce begins to evaporate and thicken.
When ready to serve, serve on top of corn tortillas with chopped fresh cilantro and crumbled cotija cheese.