Preheat oven to 400°F (200°C) and line a baking sheet with parchment paper.
Slice jalapeños in half lengthwise and remove seeds and membranes using a spoon.
In a medium bowl, combine softened Neufchâtel cheese, Greek yogurt, shredded cheddar, garlic powder, and onion powder.
Fill each jalapeño half with approximately 1 tablespoon of the cheese mixture.
Place crushed tortilla chips in a shallow bowl and press the cheese side of each stuffed jalapeño into the chips.
Arrange peppers on the prepared baking sheet and lightly mist with cooking spray.
Bake for 15 to 18 minutes until peppers are tender and the topping is golden brown.
Garnish with fresh cilantro and serve warm.