The Cafe of the Museum of Jewish Heritage at the tip of Manhattan. Amazing views of the Harbor and Liberty Island.
The catch is, it's only open for lunch. In the evening they rent it out as an event space. Here are the hours http://www.mjhnyc.org/v_cafe.html
Also, one of teh kosher but not shomer Shabbat veggie falafel places is about to open a branch in the kiosk in Central Park on the banks of the Harlem Meer. Not exactly a restaurant, but a very pretty water view. ;-)
And, while it is not what the OP needs, it is a short walk from the Jewish Museum, the Met, the Museum of the City of New York, the Guggenheim, and the rest of Museum row on Fifth Avenue. So it will be useful for many people, especially families on a museum excursion.
It's Maoz. http://www.maozusa.com/central-park