For the salsa: Heat the canola oil in a medium heavy-bottomed skillet over medium-high heat. Add the tomatoes, garlic and onions and saute until golden brown, 10 minutes. Add the chipotles and saute for another minute.
Add the skillet ingredients along with 1 tablespoon salt and 1 teaspoon black pepper to a blender and process until smooth. Return the mixture to the skillet and cook over medium-low heat for 5 minutes; season with additional salt and pepper. Keep warm.
For the tortilla chips: Heat 2 inches of oil in a large, low Dutch oven until a deep-fry thermometer inserted in the oil registers 375 degrees F. While heating, stack the tortillas and cut the stack into 8 triangles.
Working in batches, fry the tortilla triangles until crisp and golden in color, about 2 minutes per side. Remove the chips from the oil and drain on a paper towel-lined baking sheet; season with salt.
Add the tortilla chips to the skillet with the warm salsa, making sure all the chips are fully coated in the salsa. Transfer to a serving dish. Top with fried eggs if desired, and sprinkle with the queso fresco. Garnish with thinly sliced red onions, Mexican crema and chopped cilantro.