You do not have high CPU usage. Your CPU is 99.2% idle.
You have high load averages, which is not the same thing. (This provides some interesting history around this.)
A process contributes to load when it is running on a CPU, but it can also be counted as part of the load when it is waiting in state TASK_UNINTERRUPTIBLE. That can include waiting on disk IO or mutexes (and many other things).
How confident are you that logstash is causing the high load average? Does it drop when logstash is stopped? If it is logstash then I would start looking at stack traces for each thread in the JVM and try to figure out what it could be waiting on.