I’ve created a nice little bash script to take MongoDB backups that is replicaset aware.
It will only take a backup from a replica so if you have the classic master,replica,arbiter configuration you can setup the script via cron on both (current) master and replica and the backup will only run on the replica.
It will then tar.gz the backup and upload it to Google Storage. It can be easily adapted to upload the backup to S3 using s3cmd or the aws cli (aws-cli).