Depends on the lens, and what you mean by manual focus. If you mean through the viewfinder, the stock focus screen in both is the same, and is not very good for lenses faster than f/2.8 (because you'll see the DoF of ~f/2.8 even with faster lenses). The 6D has a user-replaceable focus screen, so you can easily install the Canon Eg-S, which will show you the true DoF of a fast prime (and conversely, f/4 and f/5.6 lenses will give you a pretty dark viewfinder). Canon doesn't consider the 5DIII's focus screen to be user replaceable. There are 3rd party options, installation can be easy, but also easy to screw up (misalignment resulting from improper shimming), and metering may be affected (the 6D has settings to compensate for other Canon focus screens).
If you mean manual focus via Live View, there's no difference between the two cameras. If you're going to rely on focus confirmation from the AF system, the 5DIII has an edge.