Optimal queueing control of multi-hop networks remains a challenging problem even in the simplest scenarios. In this paper, we consider a two-hop half-duplex relaying system with random channel connectivity. The relay is equipped with a finite buffer. We focus on stochastic link selection and transmission rate control to maximize the average system throughput subject to a half-duplex constraint. We formulate this stochastic optimization problem as an infinite horizon average cost Markov decision process (MDP), which is well-known to be a difficult problem. By using sample-path analysis and exploiting the specific problem structure, we first obtain an \emph{equivalent Bellman equation} with reduced state and action spaces. By using \emph{relative value iteration algorithm}, we analyze the properties of the value function of the MDP. Then, we show that the optimal policy has a threshold-based structure by characterizing the \emph{supermodularity} in the optimal control. Based on the threshold-based structure and Markov chain theory, we further simplify the original complex stochastic optimization problem to a static optimization problem over a small discrete feasible set and propose a low-complexity algorithm to solve the simplified static optimization problem by making use of its special structure. Furthermore, we obtain the closed-form optimal threshold for the symmetric case. The analytical results obtained in this paper also provide design insights for two-hop relaying systems with multiple relays equipped with finite relay buffers.