Hot Spots
There are a few places on Long Island that seem to have a much higher concentration of sightings, or that have been the location of a large scale event.
Mount Misery:
Mount Misery was used as a stopover in traveling even back in the settler days, as it was between farmland but not so arable itself. There is one hotel on Chichester Road that has been there since long before the Revolutionary War. According to an article found at http://billknell.tripod.com/alien/mountmisery.html there was also an insane asylum and a military hospital. Bill Knell was deeply involved with a group called Island Skywatch back in the early 1990s on Long Island, and even had a UFO hotline. Mary's Grave is also supposedly located in Mount Misery, as well as a few other strange urban legends.
Southaven Park:
Though I have not found a large number of sightings here, it is a Long Island "hot spot" because there was a possible UFO crash reported here back in the early 1990s. Though it is near the Mastic area, It deserves special notice. See sightings for the complete account.

Mastic / Moriches:
According to one of the top UFO researchers on Long Island, John Ford, this area is a leading source of abduction reports countrywide. According to an article on 7/2/93 in the Long Island Advance, John Ford calls it the "highest area of UFO activity in Suffolk County". Locations in this area include the Brookhaven town dump and Brookhaven National Laboratories.