Personally I would carry with the hammer down on an empty chamber. There is a slight difference in safety between the empty chamber and between chamber positions, with the 'safer' position being the former.
With the hammer in the between chamber position, the bolt is raised and resting on the surface of the cylinder, between stop notches. The only thing keeping the cylinder from rotating into the in-battery position is the hammer itself. That's perfectly safe as it would require a force sufficient to actually fracture the cylinder to rotate it.
With the hammer down on an empty chamber, the bolt is raised into a stop notch on the cylinder, thus there are two things (the hammer and the bolt) preventing cylinder rotation. While two things are better than one, as a practical matter in terms of safety this is equivalent to the same position in the between chamber case.
However, if the hammer were to be pulled back inadvertently, say by being caught on the belt or edge of a holster, the between chamber case is less desirable. In that case the cylinder will become free to rotate as soon as the hammer clears the back of the cylinder (remember the bolt is not in a stop notch), and while the hand is not yet moving the cylinder it is free to move and will be in battery after only 30 degrees of rotation. The hammer could then drop on a loaded chamber.
In the empty chamber case the cylinder will not become free to rotate until the bolt drops free of the stop notch, when hammer approaches nearly the half cock position. This is significantly further back (the exact amount depends on the gun) than the between chamber case. Further, the cylinder must rotate twice as far to come into battery.
This extra movement does provide a slight bit of additional safety when using the empty chamber method of carry. However, that must be weighed against the advantage of having the additional round available. Many people would prefer to have that bullet and eschew the slight, perhaps very slight, safety advantage. In the end, both methods are much better than the half cock position which depends on the sear remaining intact for holding back the hammer; dropping the gun is all that's necessary to break the sear and fire the bun. OOps. I meant gun.