After self diagnosing the issue, it appears as though the use of the Native API for esphomelib cannot be used in conjunction with MQTT. It may or may not be related to the warning posted here after step 9 - https://esphomelib.com/esphomeyaml/components/api.html#migrating-from-mqtt-to-native-api-setup-in-home-assistant
In my case the 5 minute recurring disconnects were the NodeMCU restarting every 5 minutes due to not detecting a connection to the Native API. So I ended up ditching MQTT and used the Native API.