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In the team’s second year, future United States national team goalkeeper Tony Meola, Chris Armas, and future Portland Timbers coach Giovanni Savarese helped the Rough Riders finish the season with a 20-2 record. Savarese would later be named the USISL regular season and playoff MVP. The wins kept on coming as the team ended up closing their home schedule 11-0 for the season, including an exhibition game against the U.S. Olympic team where the Rough Riders had a 3-0 victory In the final game against the Minnesota Thunder, things were looking to go into extra time as a minute remained and the score remained tied at 1-1. With 6 seconds left in regulation, Savarese scored the winning goal. Led by coach Alfonso Mondelo, the team won its first USISL Championship.
In 2002, the Rough Riders won the D3-Pro League Atlantic Conference with a 13–6–1 record. Derrick Etienne and Cordt Weinstein combined for 27 goals, while goalkeeper Billy Gatti maintained an imposing presence in net. Long Island squeaked past New York on penalty kicks after a 2–2 tie in the playoff quarterfinals, and enjoyed a dominant 3–0 win over the Connecticut Wolves in the semifinal to reach the championship game. The final against Southern Conference champions Wilmington Hammerheads was a tight game, but the Rough Riders emerged as 2–1 victors to take their second championship in franchise history.
