Low level answer, if you want to know the whole list:
This is stored in an sqlite3 database in Google Chrome's userprofile folder, on Linux it's located in
You can use SQLite3 to have a look at it:
me@local~/.config/google-chrome/Default$ cp Top\ Sites ts.sqlite
me@local~/.config/google-chrome/Default$ sqlite3 ts.sqlite
CREATE TABLE thumbnails (url LONGVARCHAR PRIMARY KEY,url_rank INTEGER ,...
sqlite> select url_rank,url from thumbnails order by url_rank;
To answer your question:
You can delete or edit an entry using regular SQL commands, but be sure that Chrome is not running, i.e. the file is not opened (by Chrome). Also note that I did all actions on a copy because of that (was only looking).