Virtualization as a platform for resource-intensive applications, such as MapReduce (MR), has been the subject of many studies in the last years, as it has brought benefits such as better manageability, overall resource utilization, security and scalability. Nevertheless, because of the performance overheads, virtualization has traditionally been avoided in computing environments where performance is a critical factor. In this context, container-based virtualization can be considered a lightweight alternative to the traditional hypervisor-based virtualization systems. In fact, there is a trend towards using containers in MR clusters in order to provide resource sharing and performance isolation (e.g., Mesos and YARN). However, there are still no studies evaluating the performance overhead of the current container-based systems and their ability to provide performance isolation when running MR applications. In this work, we conducted experiments to effectively compare and contrast the current container-based systems (Linux VServer, OpenVZ and Linux Containers (LXC)) in terms of performance and manageability when running on MR clusters. Our results showed that although all container-based systems reach a near-native performance for MapReduce workloads, LXC is the one that offers the best relationship between performance and management capabilities (specially regarding to performance isolation).