As I understand it, all of the monitoring involved in the NSA program involved international calls (and international e-mails). That is, the NSA was intercepting communications in the U.S., but only communications going outside the U.S. or coming from abroad. I'm not aware of any cases applying the border search exception to raw data, as compared to the search of a physical device that stores data, so this is untested ground. At the same time, I don't know of a rationale in the caselaw for treating data differently than physical storage devices. The case law on the border search exception is phrased in pretty broad language, so it seems at least plausible that a border search exception could apply to monitoring at an ISP or telephone provider as the "functional equivalent of the border," much like airports are the functional equivalent of the border in the case of international airline travel.
I’m not a legal expert by any stretch, but would this mean that any email, phone call or computer traffic could constitutionally be monitored by the government? Would the same logic be able to extend to private traffic (i.e. point to point data lines) that travel over international borders? If so, that’s more than a bit frightening.