Paragon Sports is probably the best in te city. There is a guy that really knows his shit about boots. Ive had them mount and tune my skis and they did a great job. They sell freeski hard goods and soft goods. its on 18th & Broadway.
There is REI in Soho and also EMS on Broadway in Soho. They're both ok.
Theres one on Queens Blvd in Forest Hills but its lame and there is one called Panda in Brooklyn thats slightly better.
Theres a few good ones in Nassau County.