Preheat oven to 350 degrees. Lightly spray a cookie sheet with nonstick spray.
Cut the top off of the tomatoes and gently scoop out the inside of the tomato to create a cup. Be careful not to poke a hole in the bottom or sides. Place on prepared cookie sheet.
In a skillet on medium heat, cook the bacon. When the bacon is half cooked, add the peppers and mushrooms. Cook until bacon is crisp and peppers are soft. Remove from heat, spoon mixture into tomato cups.
In a bowl, whisk together eggs, egg whites, milk, and salt, Pour into tomato cups, leaving about 1/4 of an inch of space at the top of the cup. Top each tomato cup with cheese.
Bake for 15 to 20 minutes or until egg is cooked through and cheese is melted and bubbly. Allow to rest a few minutes before serving!