I would go to JG for the anniversary dinner out of those choices. A year ago, it was EMP, but they've gotten ridiculous with the themes, gimmicks, $20 coffee, etc. It's such a shame too, because the room is the best of the three. It might be better at lunch in terms of the smoke domes and other nonsense, but I'm not sure. Daniel's food is good but I found it unbearably stuffy and I'm not a fan of the room either.
Babbo (only Batali restaurant I will recommend)
Bouley's food is good but it is hands down the worst room out of any upscale restaurant in the city.
Cafe Boulud (I like this much more than Daniel)
Lupa is not upscale and the food is bad. Try Ciano.
Marea is fantastic if you stick to the pastas...the entrees are not great there.
Luger has a great steak...but so do a million other restaurants in NYC at this point. It might have prices in line with most upscale steakhouses, but the space, atmosphere, etc. are not. Try Minetta Tavern, perhaps BLT Prime.
Toto is great.
I'm not huge on halal carts.
For burgers, you might want to try Burger and Barrel or the Spotted Pig instead. Shake Shack is good for its style and I'm pretty sure it'll be a few bucks cheaper than those two places, though.
For pizza, Motorino and Keste are great. Keste is wetter in the middle and flimsier than Motorino, so it depends on your preference. Keste has a lot of variety but Motorino's pizza menu is more focused. Sides are better as well. I'm a huge fan of Co. and Franny's (Brooklyn). Franny's definitely has the best non-pizza dishes and their appetizer menu is great. Park Slope is a great walking neighborhood too.
Kin Shop - have not been.
My lord do I have a lot of free time on my hands today.