Well, the NYT did claim that the emails were authenticated. So, if Rudy and his cronies altered them, I presume the computer forensics would show that, would it not? I'm not a computer expert, so I can't really say if it is possible to fake content on a hard drive and not have it be detected. As a minimum, they did not say that any of the content appears doctored. That's all I got for ya.
It most certainly is possible to fake content. It all comes down to how much faking you want to do. At the simplest level you can easily do it yourself: Plug in a thumb drive and copy a file to it. Notice how the file written date is the file written date of the original file, not the time you actually did it? Windows fakes the file date for your convenience, making it match the original instead of telling the truth. (And it most definitely is faking it--if you look at the new file while it's still writing it you'll see it has the current time. Once all the data is written it then copies the file timestamps over.)
Such fakery can only be detected when either the fakery is inconsistent (what often happens with photoshops--for example, pasting together two images that had light sources from different angle(s)--that's very hard to correct for) or when they leave behind signs of the tampering.
That's why programs like PGP exist--without a digital signature there's no way to know if it's real or not.