I think Ezra Klein sums it up pretty well:
"If the New York Times has evidence that John McCain conducted an affair with a lobbyist, then they should come out and say so. To try and imply it primarily by reporting the concerns of members of McCain's staff and halfhearted denials from his allies is confusing for the reader and bad for the paper. They don't get to create plausible deniability by hiding the charges in a much longer exploration of McCain's reputation for honesty and his history with lobbyists and special interests -- the substance of the story is whether McCain had an affair with a lobbyist, and whether he then advocated for her clients improperly. Those two things either happened or they didn't, and the paper should just tell us which it is."
It wouldn't suprise me in the least if McCain had an affair but the Times has not documented that. The NY Times has trotted out a piece more becoming of the Enquirer than of the Paper of Record.