The Northern Dispensary, originally built to care for the "worthy poor," still has stood vacant for years partly because its use is limited to that of a medical clinic—but also because it's owned by the Gottlieb estate, which is notorious for buying properties and sitting on them.
The Infamous Abandoned Properties Below 14th Street
This is an article I've been meaning to post; the New York Press is a free local newspaper, and this was their cover story on a recent issue.
The article showcases several properties, some of which have been standing vacant for years, but a curious omission is one building I can see from my apartment and which has been empty for over ten years: the former P.S. 60, which was called "CHARAS" for over ten years, until it was sold at auction and has been warehoused ever since.