No, not where to *buy* lunch--where to sit and eat what you already have. Current inclement weather notwithstanding, spring is on the way, so outdoor places are preferred...but any pleasant spot to sit and eat lunch is most welcome.
Here are some of the spots in my current rotation:
Citicorp Plaza: access is now only through the main lobby (since Sep 11), and you have to sign in and show ID, but the benefit of that is that it's much less crowded than it used to be; some days, I'm the only one eating there. It's a vexillologist's dream, with all of the flags of the United Nations (as of 1995, the 50th anniversary) hanging from the (glass) ceiling.
Atrium, 2nd & Mission: this is indoors but not claustrophobic--lots of glass gives it an open feel--so it's perfect for rainy days. There are tables and chairs at street level and on a mezzanine level.
Crocker Galleria: the roof garden is nice (if crowded at lunchtime), but there are no tables, so anything less wieldy than a sandwich could be problematic. There are plenty of tables & chairs inside the galleria, but it's not quite as pleasant.