Neither will provide a big gain in HP, the shorties will probably get you 6-8 HP (from tests I've seen) and the TB will get you 0-8 HP depending on who you want to believe. Also many believe the TB works better if you get a custom tune in conjunction with it.
I ran an 85mm BBK TB on my old R/T and while I never dyno tested it I thought it worked well. Never got around to putting any shorties on so no personal experience there. Here's a link to an old thread I did back when I did the TB there might be some useful information in it for you
http://www.challengerforumz.com/showthread.php?t=71162 I would probably lower the estimated HP gain numbers now though, the one's I put in the thread were what I found in several articles in various Mopar magazines at the time and were most likely overly optimistic based on what I've seen written since.
In addition to commercial shorty headers you might want to consider adding a set of used SRT exhaust manifolds as they can be had relatively cheaply and add basically the same gain.
The final factor to consider is ease of installation. The TB can be easily installed and the shorties can be a bear or if hired out certainly more costly while the TB can be done by you fairly quickly. So if you aren't doing the job yourself the cost of the header install may need to be factored into your decision.
Personally I'd do both (using a set of SRT exhaust manifolds) and grab a custom tune if possible. Good luck with your decision. :smileup: