Arrange one oven rack 6 to 8 inches from the broiler and a second rack in the middle of the oven. Heat the oven to 400?F. Line a rimmed baking sheet with parchment paper or a silicone baking mat.

Halve and thinly slice the yellow onions. Pick the leaves from the fresh thyme until you have 2 tablespoons. Mince the garlic. Grate the Gruy?re cheese.

In a large bowl, combine the garlic, 2 teaspoons thyme, 1/4 cup Gruy?re cheese, panko breadcrumbs, milk, egg, Worcestershire sauce, 1 1/4 teaspoons kosher salt, and 1/4 teaspoon black pepper. Add the ground beef and mix gently until combined.

Form the mixture into 32 to 34 meatballs (about 1 1/2-inch each) and place them on the baking sheet, spacing them 3/4-inch apart.

Bake on the middle rack until browned and cooked through (165?F), about 15 to 20 minutes. Meanwhile, prepare the sauce.

In a skillet, melt the butter over medium heat. Add the onions, 1 tablespoon thyme, remaining kosher salt, and black pepper. Cook, stirring frequently, until the onions are soft and deep golden-brown, about 25 to 30 minutes.

Sprinkle flour over the onions and stir until incorporated and begins to brown, about 1 minute. Add white wine and scrape any browned bits from the skillet, stirring until the wine evaporates (about 30 seconds).

Add beef broth and whisk to combine. Increase heat back to medium, bring to a boil, and cook until sauce thickens (6 to 8 minutes). Stir in vinegar and adjust seasoning as needed.

Remove the meatballs from the oven and set the oven to broil. Transfer meatballs to the sauce and gently stir to coat, then spread into an even layer. Sprinkle with remaining Gruy?re cheese.

Broil in the oven until cheese is melted and bubbly (3 to 4 minutes). Garnish with remaining thyme leaves and serve with crusty bread, if desired.