This paper presents a comprehensive survey of the existing blockchain protocols for the Internet of Things (IoT) networks. We start by describing the blockchains and summarizing the existing surveys that deal with blockchain technologies. Then, we provide an overview of the application domains of blockchain technologies in IoT, e.g, Internet of Vehicles, Internet of Energy, Internet of Cloud, Fog computing, etc. Moreover, we provide a classification of threat models, which are considered by blockchain protocols in IoT networks, into five main categories, namely, identity-based attacks, manipulationbased attacks, cryptanalytic attacks, reputation-based attacks, and service-based attacks. In addition, we provide a taxonomy and a side-by-side comparison of the state-of-the-art methods towards secure and privacy-preserving blockchain technologies with respect to the blockchain model, specific security goals, performance, limitations, computation complexity, and communication overhead. Based on the current survey, we highlight open research challenges and discuss possible future research directions in the blockchain technologies for IoT.