In MarkLogic 7, we introduced a new History Monitoring APIs and a dashboard to help you visualize the performance over time. These features are described nicely in our docs.
But, if you're still running MarkLogic 6, we've also made available a tool we've used in house called mlstat
mlstat is a command line tool that monitors various aspects of MarkLogic Server performance on Linux. It runs on the MarkLogic node itself and is modeled on the classic Unix tools like vmstat and mpstat. It is designed to be always on, running in the background redirecting it's output to a file. It has the ability to tag each line of output with an Epoch or timestamp so the data can be correlated with an event.