Hi! Someone mention my name?
I'll third on the Pike Place Market. It can be a lot of fun (well, no pinball, but there are still places in there that will blow your mind). You can see the Space Needle from nearly anywhere in the north downtown area. I work about three blocks away from the Needle.
The Underground Tour is best done as an evening excursion. Hopefully you can get the bawdy version of the tour and find out how Seattle REALLY got its start.
The Seattle Pinball Museum (it's a business, actually) is in the International District (Asiatown), you want to visit there later in the week. Mostly afternoons and evenings. 34 pins there now.
Shorty's is open every day from noon to 2AM, so you can easily plan other things around that. 17 pins there.
Chocolate tours. Hmm. There's the Theo Chocolate place in Fremont that does tours, they make some damn fine chocolate. Not to mention there's Brouwer's Pub just up the street from there and that's where the serious beer drinkers go. Good restaurant too. And, afterwards, if you look across the street and see a line of mopeds and scooters off the alleyway and a big door open, go there to ADD Motorworks and ask Brad if you can play some pinball. There's three in the front (Stern Stars, Stern Big Game, and Stern Dragonfist) plus some more in the back room.
Let me know when you're in town. I'd like to meet up with you, perhaps for lunch?