This is Jonathan Lethem’s This Shape We’re In.
Lethem, author of the bestselling Motherless Brooklyn , returns in
concentrated form - packing twice the adventure into one-eighth the
pages. This book could be some kind of allegory book, but it might not
be an allegory book at all. It involves people and drinking and people
looking for a giant eye. It is among the best things Mr. Lethem has
There's a review here that gives some additional detail, mentioning the spaceship (of indeterminate form) and the quest for the third eye.
The book concerns the activities of Henry Farbur, a cretinous drunk of
an Everyman who lives in the bizarre world inside a Shape of somewhat
indeterminate biological form-- Henry and his wife have a burrow in
the bowels, while there's a cathedral in the left lung, and so on. The
purpose of the shape is a subject for much speculation among the
inhabitants-- religions have sprung up asserting that it's a bomb
shelter, or a generation starship, or something else entirely.
There's some snappy writing here, as Henry and his stooge Balkan
embark on a quest to find the third eye, with Henry abusing everyone
he encounters verbally and otherwise. The final revelation of the
purpose of the Shape and the red phones from Central Command was
unexpected and clever, which counts for something, but I'm still not
entirely sure what the point of the whole thing was.