Healthy in Midtown
ORganic Harvest- they changed their name recently but they are at 235 E 53st. near 3rd. Decent sandwiches good veggie chili, and salads, also some interpretations of Indian and Asian dishes. Also some macrobiotic options. Their stuff is pretty fresh and I believe, they use organic ingrdients for most dishes. http://www.organicharvestcafe.com/
There is also a deli on second street in the mid forties (west side of street) that had organic goroceries and an organic salad and hot food bar. They had limited selections but they were quite tasty. I haven't been in a few years since I changed jobs.
Westerly foods on 8th ave and 54th has a good selection of homemade organic soups - generally vegetarian. They are very tasty. Also, they have a good selection of sandwiches in the deli case.