Finely dice 3 jalapenos and remove the seeds and pith. Leave the seeds and white membrane in for a hotter dip.
In a medium bowl, combine 8 ounces cream cheese, room temperature, 1 cup sour cream, jalapenos, 1 shallot, finely diced, 1 1/2 cups shredded sharp cheddar cheese, 3/4 cup shredded pepper jack cheese, 3/4 teaspoon salt, and 1/4 teaspoon black pepper. Mix until well combined.
Transfer the mixture to a small oven-safe baking dish and smooth the top.
Place the tortilla chips in a plastic bag and crush with a rolling pin to a coarse texture.
Top the dip with 1 cup crushed tortilla chips.
Bake for 30 minutes, until hot and bubbly around the edges.
Remove from the oven and sprinkle with 1 tablespoon chopped fresh cilantro. Serve hot with tortilla chips.
Notes
Make-Ahead: Prepare the dip up to 2 days in advance and refrigerate. Hold the tortilla chip topping separately and add just before baking. Add 5-7 minutes of extra bake time if baking from cold.Leftovers: Store covered in the refrigerator for 3-4 days. Reheat at 350 degrees F for 15 minutes or in the microwave in short bursts. Add fresh cilantro after reheating.