I figured it out. My final yaml is:
version: "3"
services:
elasticsearch:
image: elasticsearch
ports:
- "9200:9200"
- "9300:9300"
kibana:
image: kibana
ports:
- "5601:5601"
links:
- elasticsearch
depends_on:
- elasticsearch
logstash:
image: logstash
links:
- elasticsearch
volumes:
- ./:/config-dir
command: logstash -f /config-dir/logstash.conf
depends_on:
- elasticsearch
The command line is what I needed to add.