Yes, this is a short list.   To make the list, the store has to give you good advice on what all shoe to wear.   Most are are staffed by runners. 

Runners Edge 242 Main St; Farmingdale, NY; Toll Free 877-RUN-EASY (877-786-3279)

Schwab's Second Wind 1371 Rt. 25A East Setauket 631-751-5534

Super Runners Shop 355 New York Ave; Huntington; 631-549-3006

Gubbins Perfect Fit 54 Park Place, East Hampton, 631-324-3239

Quantum Feet 188-13 Union Turnpike Fresh Meadows, NY 11366 Tel. (718) 454-3338

Sayville Running Company - 55 Main Street; West Sayville, New York; Tel 631 589-5700; Fax 631 589-5701

Lynbrook Runner's Stop - 20 Atlantic Avenue, Lynbrook, NY 11563; 516 568 7333

Rubber Sole Running - 35 East Main Street Babylon, NY 11702; 631.482.1914

Not great but cheap:
Outlets Stores:

• Nike Outlet; 790 Sunrise Hgwy; Bellport; 516-286-0112
• Reebok Outlet; Tanger Factory Outlets;1770 W. Main St.; Riverhead; 631-727-7000
• DSW Shoe Warehouse; 1819 East Jericho Turnpike, Dix Hills