This list is subjective of course, I read a lot of great books this year, when I started typing these are the first eleven that jumped into my brain, in no particular order. The fact that these all stuck with me is telling, they are damn good reads. I loved all of these and suggest if you haven’t read them that you should.
Meg Gardiner PHANTOM INSTINCT
(Dutton)
Gregg Hurwitz DON’T LOOK BACK
(St. Martin’s)
John Connolly THE WOLF IN WINTER
(Atria/Emily Bester)
Laura Lippman AFTER I’M GONE
(William Morrow)
Blake Crouch THE LAST TOWN (part three of Wayward Pines Trilogy)
(Thomas and Mercer)
Sam Cabot SKIN OF THE WOLF
(Blue Rider Press)
Rob Brunet STINKING RICH
(Down and Out)
Chelsea Cain ONE KICK
(Simon and Schuster)
Jennifer Hillier THE BUTCHER
(Gallery Books)
John Verdon PETER PAN MUST DIE
(Crown)
Tim Hallinan FOR THE DEAD
(Soho)
These books are all available from great indie mystery stores, like Once Upon a Crime in Minneapolis, Murder by the Book in Houston, Poisoned Pen in Arizona, Mysterious Galaxy in California and The Mysterious Bookshop in New York. (Click on a name to link to the store)
Meg Gardiner PHANTOM INSTINCT 
Tim Hallinan FOR THE DEAD