Hot Chocolate definitely is the right choice for dessert; the Chef Mindy Segal, was formerly the pastry chef at MK in its heyday.*
As for your choices, Cafe Bolero is a little casual for a special night out and the food is so-so, in my opinion.
I think Cafe Matou is fantastic, but as you've nixed the type of food (French bistro) then I would also nix Cafe Absinthe as its food is similar.
Which leaves Baccala, which is the best choice in my book. I had a nice meal there a couple weeks ago, much more enjoyably simple in concept and execution than even a meal I had had previously at Timo, the associated "fancier" restaurant by the same chef/owner. Service is casual, but friendly and efficient, and the atmosphere on a Tuesday should be calm, quiet and relaxing.
After dinner, you could also head around the corner and have a nightcap at
The Violet Hour.
*This is not to say that MK has gone downhill, but there was a time when it was the hottest restaurant and M.S. was part of that.