I dove both - Lembeh and Ambon.
Lembeh (3 times) stayed in Bastianos - good management, exelent dive guides (Yap, Oppo, Ranto).
Ambon (1 time) stayed in Blue Rose - more cheap than DIA and Maluku and they are located just in Laha. Accommodation is budget, but i had everything I need (bed, hot...