Prepare the onions, celery, potatoes, and carrots. Add to a large pot.
If you are using clam bouillon, add enough bouillon to flavor a total of 3 cups of water. Stir into the vegetables. If you are using clam juice (either packaged separately or from the canned clams), add directly to the vegetables.
Add just enough water to cover the vegetables. Spice with the thyme, red pepper flake (optional), salt, and pepper. Cook over medium heat until the potatoes are tender (about 20 minutes).
In a small pot, melt butter over medium heat.
Remove from heat. Mix the flour into the butter until a smooth paste has been made. Slowly add the half and half by thoroughly mixing small splashes into the flour until the roux has thinned. Return to heat. Stir in the milk. Stir continuously until thick and smooth.
Slowly stir the roux into the soup. Heat through, but do not boil.
Add the clams about 3 minutes before serving. If they cook too much they get tough. When clams are heated through, stir in the red wine vinegar and season to taste with salt and pepper.