Preheat oven to 400°.
Bring the water to a boil in a large saucepan; add onions. Cook 3 minutes or until tender; drain. Place onions in a 13 x 9-inch baking dish coated with cooking spray. Combine vinegar, honey, salt, and pepper. Pour vinegar mixture over onions. Bake at 400° for 1 hour and 15 minutes or until golden brown, stirring occasionally.