I have both, and I would highly recommend the Freak system. It works perfectly on my Shocker and I have always had a good fit. In the end though its personnal preference. If you can borrow the barrels and see which ones work best for you.
I have tried both of the barrels and different series of each I have tried the JT in normal and Avalanche series and the Boomy in Titanium and Ultralite and Ironmen Series but the ony main factor between the different types of boomys is their weight, and thats why your paying more, for a lighter barrel!! But the advantage over the Boomy with the JT is that it is interchangeable with back and front bits so you only need to buy 3 barrels where as Dye has not made an interchangeable barrel (as YET!!) so it is cheaper although the JT is the weight of a Standard Boomy but has not advantges in accuracy that I have seen vast differences if at all!!!!