Hello all,
Thank you for all of your suggestions! I'm too tired at the moment to write up a full trip report, but I went to many of the places you all suggested and had a wonderful foodie trip. Ill give a little blurb about everywhere I went.
Shopsins - Was so good, I went back twice. Just amazing food. I wish I had more words to describe it, but if I lived in new york, I think I would eat Mac n' Cheese pancakes for every meal.
Momofuku Ssam - The daily special grilled octopus might be one of the best things I've ever tasted.
Momofuku Noodle - I'm sorry Tampopo, but my heart no longer belongs to you. Best Ramen I've ever had.
Momofuku Milk - Ehh, cereal milk is interesting? That being said the cinnamon bun pie was easily the best dessert we had on the trip
Pegu Club - I went here last year and didn't much care for it. This year my opinion really changed. It had some interesting
inventive cocktails, and the Tantris Sidecar was the most interesting riff on a sidecar I've ever had.
Please Don't Tell - I really really enjoyed this place. The atmosphere was exactly what I'd hope for in a 'speakeasy' style place, and the drinks were phenominal.
Angel's Share - The 'looser' of the bars we went to. Still very good, but I didn't feel like the bartenders really had a whole lot ability themselves, besides executing the recipes they were given. My manhattan was far too boozy (looked to be a 6:1 ratio of rye to vermouth. at $15, I would have preferred Carpano to (what appeared to be) Stock). The other drinks, inversely, didn't have enough booze in them. (As my girlfriend pointed out, there is a bottle of Hypnotiq behind the bar, so how good can it be?

).
Lombardi's Pizza - They stand by being the first pizzeria in New York, and I really really enjoyed this place. It felt like a 'hood' pizza
joint, but with a crust that rivaled Spacca Napoli. I think I still prefer the toppings, etc at S.N. but this was very very nice.
Shake Shack - Went to the location on the upper east side and then ate in Central Park. Excellent shake, excellent burger. Long line.
Mesa Grill - Excellent dinner here after seeing a show. Roasted corn soup might be the best soup I've ever tasted.
David Burke Townhouse - Best service I've ever had. Amazing pretzel crab cake appetizer, and mint chocolate chip cake dessert.
Morimoto Sushi - Went here for lunch. The best quality fish I've ever tasted (note I haven't made it to Katsu yet, so this could change). The bathrooms were just amazing.
Katz Deli - Didn't really like it here. Pastrami was good, but I got frustrated with the ordering process and price.
Nanoosh Hummus - Hummus chain in NYC. Good hummus and wrap. Very bad service. Almost left without paying after waiting ~25 minutes after eating without being acknowledged.
Il Labratorio Del Gelato - Biggest disappointment of the trip. Every thing we had was very good, but didn't have any of the interesting flavors listed on the website.
Sarabeth's - Great brunch, wasn't very interesting food compared to brunch places in Chicago (Southport Grocer, Orange, etc), but executed very well and had an excellent atmosphere.