Out of the box, the MMS67 is probably a better buy.
The rubber on the MMS67 is shinier, matching his look in "Batman Begins." The rubber on the ToyFair is duller, matching his look in "The Dark Knight." However, the rubber on that second figure also had some problems with flaking for some people. Perhaps careful handling avoids the issue (I haven't had any issues), but it does seem to be more fragile than the MMS67.
The second headsculpt is much better on the ToyFair, if that matters to you - but you're probably doing a Batman pose anyhow, so the cowl is what counts, and both are great.
The accessories differ between the two - frankly, I think the pneumatic mangler (from the MMS67) is a cooler accessory than the extra harnesses for the prototype suit (from the ToyFair), which doesn't result in a screen-accurate look anyhow (the harness from the Takara Batman at least hides the Bat-logo when using it).