Combine 1 tablespoon diced shallot, the tomatoes and half of the cilantro in a small bowl; set aside.
Melt the butter in a medium saucepan over medium heat. Add the remaining diced shallot, the serranos, jalapeno and 1/2 teaspoon salt and cook, stirring, until the shallots are tender, about 3 minutes.
Sprinkle the flour into the pan and cook, stirring, until completely absorbed, about 1 minute. Whisk in the milk and bring to a simmer; cook, stirring occasionally, until slightly thickened, about 4 minutes. Stir in the pepper jack and American cheese until melted, then remove from the heat; stir in the remaining cilantro. Transfer to a bowl and top with the tomato mixture. Serve with chips.