1) Create an S3 bucket. Remove all permissions from it
2) Create an IAM role - give it explicit read permissions to just that bucket (there's a HOWTO at the bottom of this article: http://mikeferrier.com/2011/10/27/granting-access-to-a-singl...). When you start an ec2 instance, you can give it one (and only one) IAM instance role.
3) Put your secrets or configs in a file on that bucket. For example, config.json or whatever format you choose.
4) On your instance or container, use the aws-cli on when your app starts to copy that file down from S3, then read it into memory in your application and then delete it.
It's a bit of a hack but you can now easily restrict access to that secrets bucket, and only your running instances/containers can access it. The secrets only exist in running app memory. Now don't allow SSH access to those instances :)