I think there are a couple things that you have to think through when contemplating one method over another.
As B2B says, you have to have the car higher if you intend to pull the transmission with the engine. That impacts the engine hoist you select, as well as ensuring that the building you intend to use has sufficient height to accomodate that extra height.
Also, when the unit comes out, you'll probably dribble transmission fluid out of the rear transmission seal, unless you've already removed the driveshaft, and (assuming that you'll replace the u-joints while you're at it) removed the yoke from the shaft in order to plug up the tailshaft.
The transmission has to clear the body. It isn't fun when you lose track of where the tailshaft went, and while you're paying attention to the engine, the assembly rotates, and crashes into the car's body (don't forget that the body is moving up as the load is relieved by the assembly removal).
When the assembly is removed, what do you intend to do with it? How are you going to secure the unit while you're separating the engine from the transmission?
When I was doing this kind of thing on a routine basis, I preferred removing the transmission first, and then dealing with just the engine. I could get the tranny out, set it to the side, and concentrate on one 500 pound lump instead of a bolted together 600 pound lump. I would have the engine stand ready, and get the engine secured as soon as possible.
I don't think one method is inherently 'better' than the other - it kind of boils down to what you feel comfortable with. The biggest thing is to plan what you intend to do, and then do it.
There's no fun in getting the job half done and finding that you overlooked some detail, resulting in damage to the car, or damage to your body, and lost time as you regroup and start over!
Steven