For the guacamole layer, first, in a small bowl, combine the white parts of the green onions, jalapeno, garlic and lime juice. Let sit for 30 minutes or while putting the other layers together.
For the bean layer, pulse black beans, garlic, 2 teaspoons lime juice, chili powder, and 1/4 teaspoon salt in a food processor until mixture resembles a chunky paste. Transfer to a glass 8X8 or 9X9-inch dish or similar sized bowl, spreading into an even layer.
For the sour cream layer, quickly rinse and wipe out the food processor and pulse the sour cream, 1 cup pepper jack cheese cheese and 1 cup sharp cheddar cheese until smooth. Dollop the sour cream mixture on top of the black bean layer, smoothing to the edges in an even layer.
Sprinkle evenly with another one cup each of both cheeses.
For the guacamole, add two-thirds of the avocado chunks to the bowl with the jalapeno mixture and mash with a potato masher until smooth. Gently fold remaining avocado into mashed avocado mixture. Gently stir in the green parts of the green onions and the cilantro. Season with salt. Spread the guacamole over the cheese layer.
For the tomato layer, in a medium bowl, combine tomatoes, jalapeno, cilantro, minced green onions, and lime juice. Stir in salt. Strain mixture through a colander or use a slotted spoon to cover guacamole layer with the tomatoes. Discard the liquid.
Spread guacamole over cheese and top with tomato mixture. Sprinkle with additional sliced green onions, if desired, and serve with tortilla chips.
The dip can be tightly covered and refrigerated for up to 24 hours.