What fun! I'd recommend:
Madison Sourdough: my personal favorite. Lots of good chocolate and butter, with a chewy texture
Graze: baked-to-order and served warm with a glass of milk
King & Mane: more chocolate than cookie, but maybe get it to go and warm it up (unless that's cheating)
La Concha: more like a sugar cookie studded with mini chips; the rest of the bakery is great, too
Commenters on our blog also like Michelangelo's (not sure where they get theirs, but I think Fair Trade has the same supplier).
Those are just the "traditional" chocolate chip cookies. If you're willing to stretch the definition, I'd suggest looking for Cress Springs Bakery at the Dane County Farmers' Market (www.dcfm.org) for an amazing Chocolate Fire cookie (with cayenne and orange).
Looking forward to hearing about your quest!