Preheat oven to 375°F. Using a melon baller or small spoon, scoop out the seeds and flesh of the tomato halves and set them aside. In a medium bowl, gently combine cheese, onions, jalapeño peppers, and bread crumbs, saving some grated cheese for topping later. Add sea salt to taste.
Place tomato halves in a buttered casserole dish and fill each with a generous helping of the cheese mixture. Sprinkle the tops of your filled tomatoes with a light layer of the remaining grated cheese. Bake about 12–15 minutes or until the tops are nicely browned.