In a large pot, cook the diced bacon over medium heat until crispy (about 5-7 minutes). Remove bacon with a slotted spoon and set aside, leaving the fat in the pot.
Add butter to the bacon fat. Once melted, add onions and celery. Cook until vegetables are soft but not browned (about 5 minutes).
Sprinkle flour over the vegetables and stir constantly for 1 minute to cook out the raw flour taste.
Slowly add clam juice while stirring continuously to prevent lumps from forming.
Add potatoes, bay leaves, and thyme. Bring to a simmer and cook until potatoes are just tender (about 12-15 minutes).
Pour in milk and cream, stirring gently. Add chopped clams with their juice.
Simmer for an additional 5 minutes until heated through (don't boil, or the clams will become tough).
Season with salt and pepper to taste, and stir in the reserved bacon.
Remove bay leaves before serving. Top with extra bacon bits and oyster crackers if desired.