RIKU just to make sure we're on the same terminology page, when you say "what is the absolute best tune" I think you're trying to ask "who is the best tuner"?
SCT is a company that makes both tuning software to run on a PC and a handheld unit used in conjunction with their tuning software to tune your truck. These tools are used by your tuner (a PC running the SCT software plugs into their handheld, and the handheld plugs into your truck). The idea here is that while your truck is subjected to specific situations (on a dyno) the PC via the handheld will read real time data and give the tuner real time feedback. He/she can then make tweaks of the parameters and retest, further tweaking as needed. Maybe an hour (or if you're really modded, it could be several hours), you've got a tune dailed in to your very specific truck. The bummer is, as you can probably tell, this is an expensive way to go; you need to hire someone's expertise, they need to have purchased (the expensive) software, you need to buy the handheld and you need to buy the dyno time. Its not unrealistic to be invested $1000 before walking away happy.
The Edge device is a handheld device used to deliver a tune, tuned by someone you'll never meet on some other truck that may or may not resemble anything like yours. But, relatively speaking, its cheap. A couple hundred bucks and you're done.
The former scenario is by far the best option; SCT makes the tool and you find someone you're comfortable with using it (a "tuner"), to develop a custom tune for your truck. There are hundreds of highly qualified tuners across the country; SCT can direct you to several folks in your area.
Applying a tune via the Edge device is ok, but by no means is it the best way to go since your specific truck (with your mods) was not in front of the tuner, when he/she was developing the tune you just applied.
So back to your JDM reference; I cannot comment on JDM as a tuner since i have no personal experience. However I have heard several good and bad things. Its worth doing a little more research I think, at the least. Having said that, lets say you decide to go with them. How will the tune be delivered? Will JDM have your truck on their dyno, developing a tune specific for your mods (aka my first scenario?) Or will they be selling you the SCT device with a premade tune on it (aka very similar to my second scenario)?
The former is a very good way to go. The latter is probably little better than the Edge device.