In a large pot, cook the bacon, stirring occasionally, over medium-high until crispy, about 8 minutes; transfer to paper towels. Pour off all but 3 tbsp. drippings.
Add the onion to the pot and cook, stirring occasionally, over medium-high until soft, about 5 minutes. Sprinkle the flour over the onion and cook, stirring often, until the flour is well incorporated, about 2 minutes. Add 4 cups milk and stir, scraping up any browned bits from the bottom of the pot. Add the potatoes and cook until tender, about 10 minutes. Add the remaining 1 cup milk, if desired, for a thinner chowder.
Add the fish and corn and simmer over medium until the fish flakes easily, 3 to 5 minutes. Gently break the fish into bite-size pieces.
Divide the chowder among bowls. Top with the chives and bacon. Serve with crackers.