It all depends on what you want from your Jeep. There is very little difference between the early chain drive and the later gear drive engines -- everything is the same except the distributor, oil pump, and cam. The heads my be non-ribbed on the military and early CJ engines.
I have a newly re-built chain drive (they were used up until motor 44,XXX - late '46) that is going into my '47. I also have the original gear drive engine for my '47, which I will probably rebuild next year.