Preheat oven to 350. Line a 12 muffin tin with muffin liners, spray with non-stick spray.
Combine both flours, baking soda, baking powder, salt, and cinnamon in large bowl and mix to combine.
In a separate bowl, whisk together mashed banana, ¾ cup brown sugar, eggs, Greek yogurt, crushed pineapple, oil, and 1 tsp. vanilla together until well combined.
Mix wet and dry ingredients together until just combined to avoid over-mixing.
Fill each muffin cup about ¾ of the way up with the batter.
Mix together cream cheese, 2 tbsp. brown sugar, and ½ tsp. vanilla in a small bowl. Microwave cream cheese mixture for about 30 seconds to further soften.
With a ½ tsp. measuring spoon, top each muffin cup filled with batter with the cream cheese mixture.
Take a toothpick and swirl the cream cheese mixture with the muffin batter.
Top each muffin with 2 pecan halves.
Bake for 20-22 minutes or until a toothpick can be poked into the center of the muffins and come out clean.