Built on a hill sloping down to the water is the restored 18th-century village of Stony Brook. Though a popular tourist destination, complete with shopping malls and an ultraclean feel, Stony Brook has managed to retain a rural character and is an enjoyable town in which to meander. Just outside of town is Stony Brook University, part of the SUNY system, which adds to the vitality of the village.
Much of Stony Brook’s charm is due to a man named Ward Melville, owner of the Thom McAn shoe company. Back in the 1940s, Melville—concerned about encroaching suburbia—had the village rebuilt along historical lines while at the same time successfully fighting for strict zoning codes. He paid for much of the rebuilding himself.
Along Main Street are the harbor and Village Center (www.stonybrookvillage.com ), where well-marked signs point the way to shops and historic sites. To one side is an old U.S. post office, equipped with a mechanical eagle that flaps its wings every hour on the hour. To the other side is the Three Village Inn (150 Main St.), built in 1751. Once the home of Capt. Jonas Smith—Long Island ’s first millionaire—the rambling white house is now a historic inn.
Beyond the post office is the All Souls’ Episcopal Church, built by architect Stanford White in 1889. Pitched on the steep slope of a small hill, the tiny church—complete with zigzagging steps and a narrow steeple—has a fairy-tale quality, as if it were built for elves.
Continue walking a few blocks past the church to wide, dark Mill Pond and the gray-shingled Grist Mill (Harbor Rd. off Main St., 631/751-2244, noon–4:30 p.m. Wed.–Sun. June–Aug., noon–4:30 p.m. Sat.–Sun. Apr.–May and Sept.–Dec., adults $2, children $1). Built in 1751, the mill has been restored and still grinds corn.
Formerly known as the Museums at Stony Brook, this nine-acre complex (1208 Rte. 25A, 631/751-0066, www.longislandmuseum.org , 10 a.m.–5 p.m. Fri.–Sat., noon–5 p.m. Sun., adults $9, seniors $7, students and children 6–17 $5) on the outskirts of town focuses on American history and art.
Foremost among its museum buildings is the renowned Carriage House, which contains about 90 horse-drawn vehicles ranging from hand-painted coaches and fire-fighting equipment to elaborate sleighs and a very rare Roma wagon. Roma wagons seldom survive because of the Roma custom of burying all of a person’s possessions after his or her death—even wagons.
The Art Museum holds both changing exhibits and a large collection of works by William Sidney Mount, a 19th-century African-American painter from Stony Brook who depicted rural Long Island  life. The Bayman’s Art Gallery of history features hand-carved antique decoys and 15 miniature period rooms. Also on site are a blacksmith’s shop, barn, one-room schoolhouse, and other 19th-century buildings.
The lovely Three Village Inn (150 Main St., 631/751-0555, www.threevillageinn.com , $129–209 d) offers period antiques, fireplaces, ceiling beams, and plenty of Colonial atmosphere in a setting overlooking the water. Some of the rooms are housed in the historic, white-clapboard main building; others in an attractive modern wing. An adjoining restaurant (Restaurant Mirabelle, 631/751-0555, $17–36) specializes in old-fashioned American dishes such as New England lobster pie and clam chowder, served by waiters in Colonial garb.
A good restaurant choice for families is the Brook House (in the Village Center, off Main St., 631/751-4617), serving everything from burgers and sandwiches ($6–8) to dinner entrées such as steak and chicken ($13–15).