The Clockwork frameset may be marginally better, but they're both Cromoly, which is good. Nashbar is just a little more vague about it. The wheels are definitely better on the Nekkid. Sealed bearings are awesome. I know on my Windsor (a The Hour, but probably comparable) the wheels are something I changed out because the stock ones were junky (not all the spoke nipples can even be turned because some are just round). The pedals look much better on the Nashbar, as the Windsor stock ones are at most not usable or at least frustrating to get into.

From my perspective the Nekkid looks the better deal as you won't have to change much on it from the get-go.