Preheat the oven to 425 degrees F. Spray a 1½-quart baking dish with non-stick cooking spray and set on a foil-lined baking sheet; set aside.
Heat the oil in a large skillet over medium-high heat until it is shimmering. Reduce the heat to medium, add the onion and salt, and cook, stirring, until the onion is softened and translucent, 4 to 6 minutes. Add the garlic and chili powder and cook, stirring, for 1 minute. Add half of the black beans, the chipotles and adobo sauce, and the water, and bring to a boil. Cook until the liquid reduces by about half, 2 to 3 minutes.
Transfer the bean mixture to a food processor, add the vinegar and process until smooth, scraping down the sides of the work bowl as necessary. Allow the mixture to cool for 5 minutes, then transfer to a large bowl. Add the rest of the beans, the tomatoes, corn, half of each of the cheeses, and ½ cup of the cilantro. Mix well and season to taste with additional salt and pepper, if needed.
Transfer the mixture to the baking dish and sprinkle with the remaining cheese. Bake until the cheese melts and browns around the edges, about 15 minutes. Sprinkle with the remaining cilantro and serve with tortilla chips.
This dip is medium-level spicy. If you'd like it less spicy (mild-level), then omit the chipotle chiles and just use the adobo sauce. If you want to eliminate heat altogether, then also omit the adobo sauce.
Leftover chiles or adobo sauce? You can freeze the individual chiles by flash-freezing them on a parchment-lined baking sheet, then store them in a zip-top freezer bag for up to 3 months. The sauce can be frozen in an ice cube tray, then transferred to a zip-top freezer bag and also stored for up to 3 months.
Make-Ahead: You can assemble this dip up to 2 days in advance. Cover with plastic wrap and refrigerate until ready to make. You may need to add an extra 5 minutes or so to the bake time if refrigerated in advance.
Freezer-Friendly: This dip freezes really well! You can freeze in an airtight container for up to 3 months. Thaw in the refrigerator overnight, then reheat in a 350-degree oven until warmed through.