Node identification is the first line of defense for the security of wireless Internet-of-Things (IoT), which prevents illegal devices from accessing the network and launching attacks. Hardware features originating from innate hardware manufacturing imperfections are considered promising fingerprints for identification; among which, the hardware clock feature has been put under the spotlight due to its practicality and ease of extraction. However, current extractions of hardware clock features over wireless networks rely on the transmissions of time information, which, per se, enable significant vulnerabilities such as spoofing and replay attacks. In this paper, we propose a covert method to extract the hardware clock features, which does not rely on the insecure time information transmissions that are adopted in most existing schemes. We also analyze the security of the proposed covert extraction. We further propose SNICK, a secure node identification scheme based on our tailored implementation of covert clock feature extraction and machine learning. We implement and evaluate the proposed approach on a real IoT testbed consisting of a Long Range (LoRa) gateway and heterogeneous end nodes. We conduct experiments to prove the security of the proposed scheme and evaluate the proposed scheme under three scenarios: short-term, long-term, and cross-environment. Experimental results of three scenarios demonstrate average identification accuracies of 98.53%, 85.9%, and 88.3%. We further reveal the identification performance under parameter and environmental variations.