Preheat deep fryer to 350˚F.
Place first 6 ingredients for the chips into a small mixing bowl and whisk together with a fork until completely combined. Set aside.
Place paper towels over a large baking sheet.
Once oil is hot, fry in small batches, stirring occasionally so the chips don’t stick together. Fry chips until barely golden brown and crisp.
Remove chips with a slotted spoon and transfer to the paper towel lined baking sheet. Repeat until all of the tortilla chips have been made.
Spread the chips into a single layer and sprinkle with seasoning. Flip the chips and season the other side, reserving 1/2 teaspoon of the seasoning. Carefully remove the paper towels from underneath the chips and discard. Toss chips together until evenly coated.
Set aside until ready to use or store in an airtight container for up to 1 week.
For the dip: Place 1 ½ tablespoons of the butter into a skillet and melt over medium high heat. Add shallot, jalapeno and garlic and sauté for 2 to 3 minutes. Add corn and continue to sauté and caramelize for 5 to 6 minutes. Season with salt and pepper. Add lime zest and juice and continue to sauté for an additional minute. Remove from heat and fold in cilantro and chives. Set aside.
Place remaining butter into a saucepan and place over medium heat. Once butter has melted, add flour and whisk together. Continue to stir together for 2 minutes. Add milk and whisk together until no lumps remain and the mixture is thick enough to coat the back of a wooden spoon.
Remove the mixture from the heat and stir in both cheese, 1 ounce at a time, until mixture is smooth.
Fold the corn mixture and remaining 1/2 teaspoon of seasoning into the cheese mixture until completely combined. Adjust seasonings.
Pour dip into a serving bowl and top with crumbled cotija and cilantro. Serve with chips and lime wedges.