I was really hoping to see Moon on this list, but perhaps it wasn't eligible? Or perhaps it was Duncan Jones' campaign to get Sam Rockwell nominated for an Oscar that distracted the nominating committee? I don't know. But two science fiction films did get nominated.
Cold Souls garnered three Spirit Award nominations, including Best Female Lead (Sophie Barthes), Best Supporting Female (Dina Korzun), and Best Cinematography (Andrij Parekh). Cold Souls is the metaphysical comedy in a reality where souls are commodities. When Paul Giamatti finds himself struggling with a performance, he puts his soul into storage only to find it's been sold.
Jemain Clement also received a Best Supporting Male nomination for his performance as scifi hack Dr. Ronald Chevalier in Gentlemen Broncos.
An honorable mention must go out to Jessica Oreck, a Truer Than Fiction Award nominee for Beetle Queen Conquers Tokyo, the documentary on Japan's fascination with beetles. While not actual science fiction, Mothra was an insect, and monster movies are a sub-genre of science fiction, right? Right.
A full list of the nominees is on the Spirit Awards website.