We debated over driving vs. taking a tour and we were really glad that we decided to do it on our own. We rented a car from Charlie's near our hotel in Carolina which was only $22 for the day, gas was only another $6. The tours I found were around $50 per person and only stayed for 1/2 a day. Driving to El Yunque from San Juan was an easy drive, I printed out directions from Mapquest or Google Maps and followed that on the way over and then followed the coastal road on the way back.
The rain forest is most definitely beautiful. The only problem is that there is not form of public transportation that goes to it, so you are gonna have to drive. If you are visiting San Juan and want to visit El Yuenque you are going to have to rent a car or take one of those tour group trips advertised through out the city.
A warning about driving. The roads are very skinny and winding. Obey the speed limits for your safety and the safety of others.
There are plenty of pull offs for you to enjoy the scenery, take advantage of them.