Chop chocolate into small pieces with a knife, or pulsing in a food processor. Whisk all-purpose flour, rye flour, baking soda, and kosher salt in a medium bowl.

Using an electric mixer on medium speed, beat butter, brown sugar, and granulated sugar in a large bowl, scraping down sides of bowl as needed, until light and fluffy, 3–4 minutes. Add egg, vanilla, and Jameson and beat until fully incorporated, about 1 minute. Reduce speed to low and slowly add dry ingredients, mixing just to blend. Fold in chopped chocolate.

Portion dough into 16 balls (about ¼ cup each - I use my ice cream scoop for this) and transfer to a rimmed sheet sheet as you go. Wrap tightly with plastic wrap and chill at least 3 hours or up to 1 day.

Position rack in middle of oven and preheat to 350°. Scrape vanilla seeds into sea salt in a small bowl and mix to combine (save pod for another use).

Divide dough balls between 2 parchment-lined baking sheets, spacing 3" apart. Flatten each ball to about ¾" thick and sprinkle with vanilla salt. Bake cookies, rotating sheets halfway through, until golden brown around the edges, 14–18 minutes (cookies will firm up as they cool). Let cool slightly on baking sheets, then transfer to wire racks and let cool completely.