The New York band's eighth studio album topped an HMV survey, as 34 organisations gave their results.
John Hirst, HMV rock and pop manager, said that the group "sounded like nothing else out there".
Hirst also revealed that the Animal Collective album is "selling steadily" after being discovered by fans "through word-of-mouth".
He added: "It's also encouraging to see indie labels doing so well, which reflects on the vibrant state of our music right now."
Fellow New York-based groups dominated the top ten, with the Yeah Yeah Yeahs, Dirty Projectors and Grizzly Bear featuring in the annual chart.
The Animal Collective LP, which received 13 nominations, could only reach number 26 in the charts when it debuted in January. It was also named album of the year in The Sunday Times, Mojo and Uncut.
In recent years, records from Arcade Fire, Daft Punk and Kanye West have topped the poll.