People that think the "manual" part in that last sentence doesn't matter should read the court order in the Yahoo case the NYT reported, where Yahoo went several rounds with NSA and the FISC to try to fight a specific FISA directive.
Note that Google, Facebook, and Yahoo have all taken pains to point out that they've pushed back on FISA directives. Which is something you can't do if the system isn't manual.
Just because they've pushed back doesn't mean the system isn't automated. It could have been a matter of "implement the automated system now, per the FISA order, and then we can have a go-round in front of the FISA court with your objections after".
This is military intelligence we're talking about here, they take their mission very, very seriously. I wouldn't be surprised if there were multiple, independent, redundant programs for monitoring this data.
† ... we think; the ultimate Constitutionality of this is up in the air.
I think that some of those people have knowledge of a secret program that enables access to the data (maybe without direct access to the servers that house it). That would make it easier to manage without having to bring all the SREs and such into the conspiracy.
I think that most of those people would not allow their lives to be destroyed with federal charges (or maybe even extralegal harassment, who knows - they do run secret prisons) in the process of reporting such a thing.
Tens of thousands of others have chosen to keep quiet about NSA's extralegal collection practices (from the contractors at the IXes installing beam splitters, to the mechanics who welded the fiber grabber arm onto the nuclear sub). Why is it such a stretch to think that 3 or 5 or 10 at Google wouldn't?
It's not even a stretch to think that NSA would have done their homework to know _which_ people inside of Google would be both able to participate and could be coerced into keeping quiet.