Add the mustard seeds to a medium saucepan and cover with at least 1 inch of cold water. Place over high heat and bring to a boil. Once it comes to a boil, remove from the heat and drain the mustard seeds, rinsing with cold water. Return the seeds to the empty saucepan.
While keeping the root intact, peel and halve the shallot. Peel the garlic clove and lightly crush. Add the apple cider vinegar, white vinegar, 1/4 cup water, sugar, kosher salt, bay leaf, both shallot halves, and the garlic clove to the saucepan. Place over medium high heat and bring to a boil. Reduce the heat and simmer on low for 17 - 20 minutes until the seeds have softened and absorbed most of the liquid.
Remove the bay leaf, shallot, and garlic from the mustard seeds and transfer to a container. Let the mustard seeds cool completely before serving. They will thicken up even more after chilling. Serve the pickled mustard seeds as a condiment alongside dishes such as pâté, smoked salmon, or cheese. Enjoy!