Yes, you can create a node.js container and upload it to your Elastic Beanstalk application instance as a zip file. You have to make sure your zip file contains the .ebextentions folder with all the required configuration.
You can find more information about the configuration of a node.js container here:
http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/create_deploy_nodejs_custom_container.html
and here:
http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/command-options.html#command-options-nodejs
Also, you can check out this blog on how to deploy "Ghost" (A node.js based blog) to Elastic Beanstalk by uploading the zip file: