Gen. Keith Alexander, asked about it at a Bloomberg event, denied the accusations. "I don't know what the report is," Alexander cautioned, adding the NSA does not "have access to Google servers, Yahoo servers." He said the NSA is "not authorized" to do this, and instead, must "go through a court process." http://www.politico.com/story/2013/10/keith-alexander-nsa-re...
while they might not have access to the "Google servers", it now is almost certain they have access to the "Google network" (i.e. fiber cable access). as seen in previous reports, intercepting sea fiber optic traffic between continents seems something the NSA has mastered...
If the article is correct, the NSA does not have that. What they have is an agreement that they can submit search terms and get matching data from a system operated by their British counterpart, GCHQ.
It is GCHQ who, per the article, has a direct tap somewhere inside Google's unencrypted datacenter-to-datacenter communications network.