How to track (non ECS) container costs on EC2?
Since you are not asking about ECS containers, this means that you must have a bunch of EC2 servers that you manage in some way (ECS/Kubernetes/Nomad/etc...). These servers are most probably included in an Auto Scaling Group.

Once you run containers on these servers, AWS does not charge you for the container. AWS only charges you per second of EC2 instance time while the instance was in a running mode.

So in fact you could say that containers are "free", you don't pay for containers, you pay for the infrastructure underneath (EC2 servers).

Netflix ICE is a great tool to track EC2 instance costs, as well as the AWS Billing dashboard.