Preheat oven to 425 degrees F. In a large skillet over medium heat, melt butter. Add onion and cook until soft, about 3-5 minutes. Add sausage and cook, breaking apart into bite size pieces, until browned. Stir in flour until completely combined then add the milk and bring to a simmer. Once the mixture has thickened, stir in the cream cheese, 1 1/2 cups cheddar cheese and 1 1/2 cups monterey jack cheese until completely combined and melted.
Fold in the cooked macaroni, tomatoes, salt and pepper and transfer to a 2-quart casserole dish. Top with tater tots, then use a spoon to create 6 wells and break eggs into each well. Top with remaining 1/2 cup shredded cheddar and monterey jack cheeses, avoiding covering the eggs. Bake until egg whites are set, about 12-15 minutes.