The TSA doesn't care what government issued ID you choose to show (if any) when clearing a checkpoint. Your airline, on the other hand, will check to see that you have the documentation necessary to allow you to enter your destination.
As for the proper documentation for a flight from the US to Puerto Rico, the answer to that
is here:
Q. Will travelers from U.S. territories need to present a passport to enter the United States?
No. These territories are a part of the United States. U.S. citizens returning directly from a U.S. territory are not considered to have left the U.S. territory and do not need to present a passport. U.S. territories include the following: Guam, Puerto Rico, the U.S. Virgin Islands, American Samoa, Swains Island and the Commonwealth of the Northern Mariana Islands.
Oh -- and the January 1, 2007 implementation date no longer counts. It was changed to January 23, 2007.