They are run by the same fine folks. Manhattan Reefs is the local (primarily) hobbyist community whereas Reefs.com is targeted at a more global audience with the goal of generating world class content via the Magazine, Blog, databases and other means and eventually providing a space for other local communities in addition to MR to interact and share.
Reefs.com is pretty new. Rather than setup local communities in other places as you suggest, the long term goal is to develop relationships with existing clubs around the country and have them nest under the Reefs.com umbrella while retaining control of their own affairs and unique identities while sharing content and resources where appropriate. That part has not happened yet--still building the content and feature rich Reefing Field of Dreams