Kubernetes DNS intermittently failing with kube-dns service and CoreDNS pods seeming OK
We also encounter this issue, but issue was with query timeout.
The best way after testing was to run dns on all nodes and all PODs referring to their own node DNS. It will save round trips to other node pods because you may run multiple pods for DNS but dns service will distribute traffic some how and PODs will end up having more network traffic across nodes. Not sure if possible on amazon eks.