The 6D will obviously be better, especially considering 5D Mark ii will be discontinued, and it doesn't have support for latest hardware, such as the 600 EX flash's group features,... etc.
The only question remain is the weather sealing for the 6D, which is still undetermined at this point. The only reason to go for 5D Mark ii would be if 6D is not sealed, and you're considering using it for pro or rugged use.