While chicken is baking, prepare jalapeno popper topping for chicken. Add bacon, jalapenos, and onions to a small skillet and fry until bacon is crispy and jalapenos and onions are tender. Remove from heat and add to a small mixing bowl. Add cream cheese, mayonnaise or yogurt, and cheeses to mixing bowl and cream together with bacon mixture until well-combined.
Preheat oven to 425º F. Place chicken breasts in a small casserole dish and bake until juices run clear when pricked, about 45 minutes.