In a large heavy saucepan cook the onion, the garlic, the jalapenos, or chipotle in butter over moderately low heat, stirring, until the onion is softened, stir in the flour, and cook the mixture, stirring, for 3 minutes. Add the milk in a stream, whisking constantly, and bring the liquid to a boil. Stir in the tomatoes. Simmer the mixture for 2 minutes. Add salt and pepper, to taste.
In a kettle of boiling salted water cook the macaroni for 6 to 7 minutes, or until it is barely al dente, drain it well, and in a large bowl combine it with the tomato mixture. Stir in the Monterey Jack and the cheddar and transfer the mixture to a buttered 15 by 10-inch shallow baking dish or 3-quart gratin dish. In a bowl stir together the bread crumbs and the Parmesan, sprinkle the mixture evenly over the macaroni mixture. Bake the macaroni and cheese in the middle of a preheated 375 degree F oven for 20 to 25 minutes or until it is golden and bubbly.