Any recommendation about run Prometheus in docker container or not?
Don't run node_exporter inside of a container as you'll greatly limit the number of metrics exposed.
There is also a HA guide in relation to Prometheus setups that may be of use to you.
Also this question would be better suited to the Prometheus user mailing list
Running Prometheus inside a container works if you configure some additional options, especially for the node_exporter. The challenges of this approach relate to the fact that node_exporter gathers metrics from what it sees as the local machine - a container in this case - and we want it to gather metrics from the host instead. Prometheus offers options to override the filesystem mount points from which this data is gathered.
See "Step 2" in https://www.digitalocean.com/community/tutorials/how-to-install-prometheus-using-docker-on-ubuntu-14-04 for detailed instructions.