Melt 3 tablespoons butter; toss with bread cubes. Place on a lightly greased baking sheet. Bake at 350F degrees for 7 minutes; turn and bake 7 minutes longer or until toasted.
Meanwhile - in a large saucepan, sauté the onions in remaining butter until lightly browned, about 12 minutes. Stir in water and bouillon; bring to a boil. Reduce heat; cover and simmer for 15 minutes.
Combine flour and 1/2 cup milk until smooth; gradually stir into onion mixture.
Stir in remaining milk. Bring to a boil; boil for 2 minutes, stirring until thickened. Reduce heat to low; stir in 3/4 cup Swiss cheese and pepper.
Ladle into four ovenproof bowls; sprinkle with reserved croutons and remaining cheese.
Broil 4 inches from heat until cheese is melted and bubbly. Garnish with chives.