Cook bacon in a medium stockpot over medium-high heat, stirring frequently, until light golden, about 5 minutes. Stir in butter until melted. Add shallot and cook, stirring occasionally, until translucent, about 3 minutes. Add wine; cook, stirring, until almost no liquid remains, about 45 seconds.
Place clams and 2 cups water in a large pot over high heat; cook, covered, until clams open, 7 to 10 minutes. Remove clams, strain liquid, and add enough water to equal 4 cups; use as stock. When clams are cool enough to handle, remove from shells and chop.
Add potatoes, stock, and thyme. Season with salt and pepper. Bring to a boil, then reduce to a simmer. Cook until potatoes are tender but not falling apart, 8 to 10 minutes. Increase heat to medium-high; and stir in clams and cream. Heat 1 minute. Season with salt and pepper; serve immediately.
