I see what you mean. It seems that it's easy to find the lists by week going back to when they started in the 40s, e.g. at http://www.hawes.com/pastlist.htm
But there doesn't seem to be a bestseller list for each year as a whole. Although - as you've probably already discovered, the NYT, like virtually every publication, does opine on the 'best books' of each year. For example this list shows their top recommendations for 2010:
And if you look on the left you'll see links to previous years.
The best alternative I can think of is Publishers Weekly annual bestsellers lists. They usually report two ways - how many weeks a book was in their bestseller charts; and also how many copies publishers report selling.
If you google something like "site:www.publishersweekly.com 2010 bestsellers" you should come up with http://www.publishersweekly.com/pw/by-topic/industry-news/publisher-news/article/45712-bestsellers-10-the-year-in-bestsellers.html
(hint by putting site:www.publishersweekly.com at the start of the search the results will show only pages on publishersweekly.com)
A similar search for 2009 brought up http://www.publishersweekly.com/pw/print/20090323/1686-bestselling-books-2009-hardcover-old-and-new-.html
The catch is that there doesn't seem to be any sort of standardization to how the information is reported from one year to another, nor is there a central page with links to past years - so it might be too much work and/or information overload if you're just looking to glance at the top 10 for each year!
Hope that helps. Has anyone got any better suggestions?