Upscale dinner in the WV - Here are the two best places:
Blue Hill
Annisa
At either place, get the tasting menu. Blue Hill is my favorite.
Sushi:
Hop on the subway and go to Sushi Yasuda. Best sushi in NYC, hands down. You won't ever get to do this in Chicago.
Eleven Madison is also terrific - order the souflee. Brunch at Balthazar is hard to beat for people watching and the food is good too. Personally, I'm not a fan of Craft but my wife is. However, I do like Witchcraft, their sandwich shop if you want to grab a quick lunch near union square.
Above all else, I recommend hopping the F train to Carroll street to eat at The Grocery on Smith Street in Brooklyn. See if you can get a reservation. Most restaurants in the west village/union square area are overrated, overpriced or touristy, and Smith Street and the Cobble Hill area are more "west villagey" then the west village itself these days. When Grocery opened the property values in Carroll Gardens went up. It's one of the best restaurants in all of new york and singly turned Smith Street into a "Restaurant Row." Most visitors to NYC stay out of Brooklyn and miss out big time.