What are the harms of noise pollution on people, generally, and
specifically those living in New York City (riding the subway train,
traffic noise, construction, etc)?  Please include long term, and
short term effects of living in close proximity to a busy
intersection, near a train, near an airport, etc.  Preference given to
answers that include high quality sources such as scientific papers,
government reports, etc.

These don't apply specifically to New York, but it may be a start.

FICAN (http://www.fican.org) has lots of documentation on the effects
of aviation noise on sleep, schools, etc.

The WHO has a document on noise which discusses the effects of noise
on community activities.
(http://www.who.int/docstore/peh/noise/guidelines2.html)

The EPA's "Levels Document" covers some of the same ground as the WHO
document, although it's much older
(http://www.nonoise.org/library/levels74/levels74.htm)

The usual effects of noise include sleep disturbance, annoyance,
interference with speech and other activities (reading, meditation,
telephone conversations, etc), and (in extreme cases) hearing loss.