Whisk flour, salt, and sugar in a bowl; work 1/2 cup unsalted butter pieces into dry ingredients with your fingers until flour mixture looks like coarse meal. Mix ice water into dough a little at a time until it just holds together. Form into a ball and press dough down to form a flat disk; wrap in plastic wrap and refrigerate at least 1 hour.
Preheat oven to 350 degrees F (175 degrees C).
Roll dough out to a circle on a floured work surface and fit crust into a 9-inch pie dish; crimp the edges.
Place onion slices into a saucepan, cover with water, and bring to a boil; reduce heat to medium and boil until onion is translucent, about 5 minutes. Drain and cool onion slices; spread into bottom of pie crust and top with Cheddar, mozzarella, and Parmesan cheeses in layers. Spread egg slices over cheese. Pour half-and-half over filling and sprinkle with black pepper.
Mix buttery round cracker crumbs and 1/4 cup melted butter in a bowl; sprinkle crumb mixture evenly over pie.
Bake in the preheated oven until browned, about 40 minutes.