Preheat the oven to 425 degrees F and place a rack on the second-to-top position.
Spread out the tortilla chips on a baking sheet in a single layer. Bake until the chips are warmed through, 2 to 3 minutes. Turn off the heat and keep in the warm oven until you are ready to assemble the nachos.
For the 3-cheese queso: Melt the butter in a large saucepan over medium heat. Add the jalapenos and cook until softened, stirring occasionally, 3 to 4 minutes. Stir in 1/4 cup of the milk to combine, and then stir in the flour to combine and cook until lightly browned and thick, 2 to 3 minutes. Pour in the remaining milk and bring to a boil over medium-high heat, and then reduce to a simmer and cook, stirring frequently, until thickened to the consistency of heavy cream, 6 to 8 minutes. Turn off the heat and stir in the cheeses until melted. Season with salt, black pepper and hot sauce.
To serve, spread out the warm tortilla chips on a large platter. Drizzle all over with the 3-cheese queso and serve immediately.