The 'Best Graphic Story' category includes two nods to DC Comics' Vertigo imprint.
Both Bill Willingham and Mark Buckingham's Fables vol 15: Rose Red and Mike Cary and Peter Goss's The Unwritten vol 4: Leviathan are in line for the prize.
Ursula Vernon's Digger (Sofawolf Press), Joe Hill and Gabriel Rodriguez's Locke & Key vol 4: Keys to the Kingdom (IDW Publishing) and Howard Tayler's Schlock Mercenary: Force Multiplication (The Tayler Corporation) were also nominated.
Phil Foglio and Kaja Foglio's Girl Genius, Volume 10: Agatha Heterodyne and the Guardian Muse was last year's winner.
This year is the fourth in which the graphic novel category has been included. The Girl Genius series took the prize on each occasion.
The 2012 Eisner Awards nominations were unveiled last week, drawing criticism for the decision to scrap the 'Best New Series' category.