Should I use AWS Elastic Beanstalk or the Amazon EC2 Container Service (ECS) to scale Docker containers?

EB vs ECS really comes down to control. Do you want to control your scaling and capacity or do you want to have that more abstracted and instead focus primarily on your app. ECS will give you control, as you have to specify the size and number of nodes in the cluster and whether or not auto-scaling should be used. With EB, you simply provide a Dockerfile and EB takes care of scaling your provisioning of number and size of nodes, you basically can forget about the infrastructure with the EB route.

Here's the EB documentation on Docker: http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/create_deploy_docker.html

With ECS you'll have to build the infrastructure first before you can start deploying the the Dockerfile so it really comes down to 1) your familiarity with infrastructure and 2) level of effort that you want to spend on the infrastructure vs the app.

Not to resurrect a dead question, but hopefully this helps someone.

The accepted answer is not clear enough: based on what OP described, OP wants ECS, not Multi-Container Elastic Beanstalk (MCEB). As far as I can tell, MCEB never attempts to efficiently pack containers into instances. OP asks in a comment, "if only one is under load, it scales only this one, or does it always scale up the instances and start all containers, no matter under what load they are ?" And the answer is "the latter"; MCEB scales up the instances and starts all containers, no matter what load they are under.

Edit

Don't use the architecture you're imagining.

How micro are your microservices? Would it be ridiculous to give them each a t2.nano? Then make them each a single-container Docker EB app - EB worker applications can be driven by SQS messages. Or use apex.run.

Edit 1/31/18:

AWS Fargate seems pretty cool.

Edit 6/5/19:

Use EKS if you need to orchestrate containers, to satisfy an itch. But really, try to avoid this. Distributed systems are hard.