Flash, as that it is one of the most widely used tools used by websites. Flash is also really good for making games, as it allows many objects to be played within a flash movie.
And for the plugins, these days most browsers already come preinstalled with the neccessary plugins to play flash.

Javascript, in my opinion, wouldn't be suitable for an entire site like that solely for animations.

As for Java, yes, and Java applets anyway can be slow.

Overall, flash seems like your best choice. I know that NBC has flash graphic novels about certain shows.

Good luck with your site!