I ended up using the Elasticsearch output to specify my 'mongoid' field
output {
  elasticsearch {
    hosts => ["http://localhost:9200"]
    index => "edb"
    #user => "elastic"
    #password => "changeme"
	doc_as_upsert => true
	document_id => "%{[document][mongo_id]}"
  }
}
info
Got the idea from this brilliant page By Sakina Shaikh