This morning we revealed the top 15 newspaper websites of 2008 as ranked by average monthly unique visitors. Now let’s take a closer look first at the top five national newspapers. (Note that the y-axis in the chart above starts at 3,000,000 uniques to get a sense of the finer fluctuations among these sites; think of it as zooming in on the top tier.) Click here for a larger version of the chart.

The New York Times’ victory isn’t surprising, but its margin of victory is stunning. NYTimes.com garnered 8,658,667 more visitors per month than its closest newspaper competitor, USAToday.com, or a difference of 80%. In 2007, the Times led USA Today by 5,033,534 or 52%. As you can see in the chart below, the breakaway began in September 2007 and, perhaps more impressively, was sustained throughout 2008.

Also notable among the national newspaper sites were year-over-year traffic increases of 54% and 60% at The Los Angeles Times and Wall Street Journal, respectively. The Journal’s rise could vindicate Rupert Murdoch’s decision a year ago to keep charging for the newspaper’s website despite complaints that its paywall was hindering traffic. (Murdoch said last week that traffic to the entire WSJ Digital Network, which includes the Journal, MarketWatch, AllThingsD, and other sites, had increased 76 percent over the past year.)

I also ran these metrics through IBM’s data visualization service Many Eyes. (It’s a good tool to keep in mind next time you’ve got data to play with.) Once you fire up the chart below, you can click to select which newspapers you’d like to compare. And if you click through to the Many Eyes site, you can also choose to look at relative growth. Let us know if you find any interesting results.