If you look at all of the textbooks, the one organization that is referenced repeatedly is ACSM (American College of Sports Medicine). That is one of the reasons that I have their cert. Their process used to be a lot more involved which I also liked. But the industry has a lot of good certifications available. ACE is also very strong and their customer services is excellent. It was probably mentioned above, but making sure that the cert is NCCA accredited is very important with employers.
I have taught NSCA and ACE curriculums to students preparing for certificaiton as well. If you are not strong on the science end of exercise, I recommend finding a good post secondary school near you for some classes. Getting some experience is also very important. You might want to check to see if any of your local gyms would let you shadow some of their trainers.
I teach instructor certification prep courses and CECs on the Big Island of Hawaii. Check out our website, www.hawaiifitnessacademy.com . I enjoy meeting and talking with people about fitness, so if you are ever coming to Hawaii, send me an email.