It has been a long time since I've worked in NYC (I'd work between 30-90 days a year in NYC) and I miss it. I normally stay around mid-town and the last time I was set to work in Brooklyn so I took the subway every day. Every morning there were 4 guys singing "This little light of mine", they were great and it was a great way to start the day.
Love Katz Deli. If you like cheese, I'd suggest hitting Murray's Cheese Bar. For beer and burgers, I like Black Tap. The best Fish and Chips for me is at the Shakespeare. I prefer dark ales to beer for the most part. Call me crazy but I like Gotham Pizza, their $5 2 slices and a can of soda lunch special was great.
If you like sandwiches and won't mind hitting Brooklyn, please go to Defontes, crazy good and huge sandwiches.
My last trip, a buddy took me to a meatball/pasta place that I can't remember the name. The spaghetti is great and it has a single meatball the size of Central Park and it was so freaking good. They had a t-shirt and a hat with a meat grinder thing...
If all goes well, I'm taking my 14 y/o next year and will tour pizza places, cheesecakes, and the M&M Store (He loves M&Ms).