I sometimes stay at Casa Cubuy. This is your backyard. Call Mary Ann at 787-874-6221. At the ariport rent a car from L & M and take it over to her lodge. Why L & M? Because they have a place in Fajardo where you can return the car. You will probably want to go over to Vieques to see the Bio bay. Thus you will return the car to L & M at Fajardo and take the ferry over to Vieques. I normally do this on the last two days of my vacation. Then I fly back from Vieques to the main airport and from there--home.
For a tour guide, if you pay my way down I will be your guide. Second best is to use Elena Harley. She lives there and knows both islands like the back of her hand. For El Yunque itself, use Robin Phillips.