Noel, the former Florida prep star who briefly played in MLS, scored early into the match for the Islanders.
The closest Puerto Rico came to adding to its lead came in the 83rd minute when Tai Atieno hit the right post.
The return match of the two-leg aggregate score series will be hosted by Jabloteh on 25 May.
The Caribbean playoff winner will join Harbour View of Jamaica and Trinidad & Tobago's Joe Public as the Caribbean representatives to the inaugural Concacaf Champions League.
The three Caribbean teams will be among 16 teams vying for eight spots in group play. Two teams from Mexico and the USA and one each from Costa Rica, El Salvador, Guatemala and Honduras earn automatic passage to the group stage.