Both approaches are problematic. One changes the magnification ratio (by altering the lens' focusing distance) without changing the distance between the camera and subject. The other changes the distance between camera and subject without changing the magnification ratio of the lens.
Which works better will vary based upon the specific qualities of the lens used and exactly how much the magnification is altered by the adjustment of the focus position of the lens.
For most well designed macro lenses, altering the camera/lens distance to the subject tends to work better than changing the position of the lens' focusing elements.
When stacking two lenses on top of each other, though, all bets are off. You're just going to have to experiment to see which yields better results. Unless you can find someone who has done technical measurements with that particular combination, you have no way of knowing how much the combination will breath (change the Angle of View) when you alter the focus position on the 105mm lens. You also have no way of predicting how much the geometric distortion contributed by the Raynox adapter will affect the advantage of one approach over the other. Even what percentage of the frame is occupied by your subject and how close to the edges of the frame your subject is can affect which approach might work better.
One thing that can be definitively stated is that trying to do this handheld will be near impossible. Regardless of the advantages/disadvantages of focus position changes versus distance changes, shooting handheld will not cut it for image stacking with macro photography.