I sincerely apologise beforehand, I know nothing about the best Indonesian historical fiction but I have some books recommendation that is related to Indonesian history; Madilog, Jakarta: Sejarah 400 Tahun, Nathaniel's Nutmeg: or, The True and Incredible Adventures of the Spice Trader Who Changed the Course of History, In the Time of Madness.

Or maybe you may try to read Pramoedya Ananta Noer’s book? (Pardon me kalau ada kesalahan, I'm not an expert in this field of knowledge)