But in a little-noticed white paper submitted by Attorney General Alberto Gonzales to Congress on January 19 justifying the legality of the NSA eavesdropping, Justice Department lawyers made a tacit case that President Bush also has the inherent authority to order such physical searches.

This wouldn't even have been in there unless they were doing it. The 4th Amendment states

The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no Warrants shall issue, but upon probable cause, supported by Oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized.

There isn't really any ambiguity in there, and the places that have been fuzzy (Miranda, searching of vehicles on the way to impound etc.) have largely been ruled on by the courts. Where is there zero ambiguity? Houses and businesses. If there is to be a search, it is done with a warrant, period.

I have zero doubts they've been doing this. It is too consistent with everything else they've done already.

USNews.com: The White House says spying on terrorism suspects without court approval is OK. What about physical searches?