From what I have googled, it seems to be best to stick to the publishing order.
From the wiki :
The Farseer Trilogy
Assassin's Apprentice (1995)
Royal Assassin (1996)
Assassin's Quest (1997)
Liveship Traders Trilogy
Ship of Magic (1998)
The Mad Ship (1999)
Ship of Destiny (2000)
The Tawny Man Trilogy
Fool's Errand (2001)
The Golden Fool (2002)
Fool's Fate (2003)
The Rain Wild Chronicles
Dragon Keeper (2009)
Dragon Haven (2010)
City of Dragons (2011)
Blood of Dragons (2013)
The Fitz and the Fool Trilogy
Fool's Assassin (2014)[7]
Fool's Quest (forthcoming, 11 August 2015)
Assassin's Fate (working title, forthcoming, 2016)