I am a huge fan of Azusa, a Japanese place on W 44th Street across from the Cornell Club. It's between 5th Avenue and Vanderbilt, right next to Grand Central Station. Get a table for 1 or sit at the bar with the many local Japanese folks who frequent there for lunch or dinner.
Then there's Cafe Habana down in Soho...one of my favorite places on Earth. It's on Prince Street on the corner of Elizabeth. There is a small bar for about six people where I've eaten by myself a lot of times.
Grand Central Station has a great little market as well as the food court in the basement...tons of options there as well.