K2DC is only partially correct about the differences between these two antennas. And I would NOT recommend his advice to "go with which ever is cheaper".
In addition to being somewhat larger and having greater power-handling capacity, the TH3-MK4 is much better built than the TH3-JR -- larger-diameter, thicker-gauge tubing, etc. -- which is evidenced by the wind-survival rating on the MK4 at 95mph, but only 80mph for the JR.
Since I had no plans to run high power, I strongly considered the JR when I first put up a beam in 1979, but decided not to "cheap out" and went for the MK (it was the MK3 at the time) despite the additional cost.
Proved to be a sound investment. It was up with not a single problem for 25 years --through numerous ice storms, a couple of hurricanes, lots of other high winds, etc. -- before it finally developed a mechanical failure in one of the traps.
After looking at the available alternatives, I replaced it with an MK4.
You can compare specs and download the assembly/instruction manuals for both antennas at the Hygain web site:http://www.hy-gain.com/Product.php?productid=TH-3MK4
The USD list price difference is only $110. Amortized over the expected life of the antenna, that's going to be no more than $5 a year.
The usual reasons for going with the JR are insufficient space to turn the full-sized MK, or inability to mount a larger/heavier antenna (e.g. must be on a light-duty tripod).
If those factors aren't in play, don't be penny wise and pound foolish.
Go for the MK.
You won't be sorry.
Mel - KS2G