One option is to go to the
%USERPROFILE%\AppData\Local\Google\Chrome\User Data\Default directory and delete the
Top Sites file (if using Chrome 14; in older versions it was called
Thumbnails), but that will remove also the other settings of the New Tab page.
A better option is to get SQLite and reset only the thumbnail data. Download the SQLite binary, unpack it to the above mentioned directory, and run the following command:
sqlite3.exe "Top Sites" "update thumbnails set thumbnail=null"
After that the icons on the New Tab page will be broken, but they will be updated after you visit each of the pages once.