Application Load Balancer can be used with Elastic Beanstalk now:
http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/environments-cfg-applicationloadbalancer.html
In order to used it your environment must meet the following requirements:
"must be in a default or custom VPC, and must have a service role with the standard set of permissions"
However when creating an environment via AWS console I haven't managed to find how to choose Application Load Balancer instead of a classic one. It has still the same option - "Load Balancer" to choose and when checked, it creates a classic Load Balancer. The only way I did managed to create an environment with Application Load Balancer is via aws eb cli as specified in the doc above:
$ eb create test-env --elb-type application
This will create Application Load Balancer. Then you will only need to configure it according your needs.