There are a number of libraries and historical societies on Long Island
with good reference collections.  You should first locate on a modern
map the locale where your ancestors lived, since repositories may focus
on their own areas. Some have limited hours and it is a good idea to
phone or e-mail in advance to be sure the local history librarian who
knows the collection best will be available. (Hours may be listed on web
sites.) I am listing below the best known collections, but the local
library or historical society in the area where your ancestors lived may
also have information. Remember, it is a long island and Suffolk County
alone is 80-90 miles in length.  Going from west to east:

The Long Island Studies Institute at Hofstra University (West Campus,
619 Fulton Ave, Hempstead, NY) has virtually all of the published books,
but its manuscript collection tends to focus on Nassau County (which was
part of Queens County until 1899).  Open M-F, 9-5; 516 463-6411.

The Huntington Historical Society has an excellent genealogical and
local history collection, but limited hours (two or three afternoons a
week); it has been closed for a couple of months because of water damage
to the building, but should be reopening within the next few weeks.
Karin Martin is their archivist; volunteers also assist and are well
informed. The library  is in their trade school building, 209 Main
Street, Huntington, NY 11743; 631-427-7045 (they charge a nominal daily
fee for non-members to use the library).

The Smithtown Library has an extensive local history collection. Richard
Hawkins and Cathy Ball are the reference librarians who are most
knowledgeable about the collection. Open seven days a week, including
evenings weekdays (1 North Country Road/Route 25A, Smithtown NY 11787,
631-265-2072).

Ditto re: Emma S. Clark Public Library (includes Stony Brook area as
well and houses the Three Village Historical Society collection),
Constance Sobel and Karin Martin (120 Main Street, Setauket, NY 11733,
631-941-4080);
Middle Country Public Library: Luise Weiss, 101 Eastwood Boulevard,
Centereach, NY 11720, 631-585-9393; and
Longwood Public Library, Cynthia Sciacca, 800 Middle Country Road,
Middle Island, NY 11953, 631-924-6400.

The Suffolk County Historical Society in Riverhead (300 West Main
Street, 11901; 631-727 2881) has an excellent genealogical and local
history collection, but limited hours (two or three afternoons a week).
It periodically issues a Register which focuses on Suffolk genealogy;
members can submit queries.  They charge a nominal daily fee for
non-members to use their library.

For government records and documents, the Suffolk County Archivist,
Sharon Pullen, is in the Office of the County Clerk, Historic Documents
Library, 310 Center Drive, Riverhead, NY 11901; 631-852-2015.

The East Hampton Library on the South Fork (159 Main Street, East
Hampton, NY 11937; 631 324-0222) has an excellent Long Island
collection. It is open afternoons and by appointment.  Diana Dayton has
been the local history librarian, but I believe she is leaving.

On the North Fork, there is at least one library with an excellent local
history collection (it may be in Cutchogue (Wendy Reeve, Main Road, PO
Box 935, Cutchogue, 11935; 631-734-6360). The Southold Historical
Society has extensive manuscripts (Geoffrey Fleming, Director, PO Box 1,
North Rd. and Maple Lane, Southold, 11971; 631-765-5500).

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Prof. Emerita, Hofstra University