The AOD is a 4-spd automatic, 4th being overdrive. The Toploader 3-speed has a 1:1 3rd gear, thus no overdrive. Both are probably equally low-performance assuming the AOD is stock.
from a performance standpoint, the aod has alot more potential...you can get it rebuilt with all the goodies, for 800.00 to 1000.00 this may sound like a lot of money, but the idea of crusing at highway speeds with your tach hanging around 2500 rpm is worth it imho... check out this website for more info http://www.baumannengineering.com/aodefund.htm
The only plus about the Toploader 3 speed is it's bullet proof, it'll be around when the AOD is scrap metal. If you have a torquey motor like a big block, the 3 speed is fine. I used to beat small block, 4 speed cars with a 390 and a 3 speed Toploader in the 1/4. And you also have to compare the two in economics, if you already have the Toploader, and you have to rebuild the AOD to use it, how much gas does the 3 speed burn over the AOD (the difference in mileage and the cost of that extra fuel) You can buy a LOT of extra fuel with the $1500 cost of an AOD rebuild.
A third pedal is so much more fun. I used to have a 65 coupe with a 289 and a three speed stick. It gave my friend's 65 Malibu four speed a good run for the money. Of course, gas was about $ .25 per gallon for premium at the time.
Is your car currently an auto? Converting a car from auto to manual or vice-versa adds cost and complexity to the swap. Certainly not enough to make up your mind entirely but definitely worth consideration.
Manuals are a lot of fun, there's no doubt, but the autos are really cool for cruising with and if setup right an auto should beat the manual in a drag race most of the time (all other things being equal and all).
If my classic had originally been a 3 or 4 speed I'd have gone with the TKO instead of the AOD. I'd say it is a toss up between an AOD and a 5-speed, but since you are talking about a 3-speed manual here I say go AOD all the way, that overdrive will come in quite handy.
I had a '67 with a 289 and a C4, hated it on the highway ( Iknow it's not an AOD). I got a '67 with a four speed, horrible on the highway. I installed a T-5, oh my god does she purrrr going down the highway. T-5 is so the way to go for a stock motor...if you want a manual