A rectangular boat. According to the book of Exodus in the Old Testament, Noah received a revelation from God to load all animals pair by pair into a huge Ark, thus saving all species from a world-wide flood. The line spoken by Kouzou Fuyutsuki in episode 26', "Will it become the Ark to save humankind from the nothingness of Third Impact?" touches upon this legend.

Source: The End of Evangelion : Glossary contained within The End of Evangelion - Theatrical Program.