The Caribbean tournament, which is taking place in six venues in Trinidad & Tobago, will qualify one team to the 2008 CONCACAF Champions Cup.
Former Colorado Rapids player Fabrice Noel scored goals in the 18th and 22nd minute to put the Islanders ahead for good. The Haiti-born Noel now has scored seven goals in four games.
Marco Velez, Jonathan Steele, Alberto Zapata, Noah Delgado and David Johnson also scored for Puerto Rico.
The Islanders had won their first-round group with a 5-2 win over Inter Moengotapoe, also from Suriname, on Thursday night.