There are many restaurants offering prix-fixe deals, too many to list all of them here. But in the front of the NYC Zagat, there are two lists: lunch prix-fixes on p. 25 and dinner prix-fixes on p. 26.
That said, here are a few excellent lunch prix-fixe options:
Fleur de Sel: 3 courses = $29. 5-course tasting = $46.
Tocqueville: 3 courses = $24.07
Jean Georges: 2 courses = $28 + $12 for each additional course.
Eleven Madison Park: Chef's daily market menu, 2 courses = $38. Add dessert = $12. 5-course Gourmand tasting menu = $58.