AWS Have release an update to https://docs.aws.amazon.com/systems-manager/latest/userguide/session-manager-getting-started-enable-ssh-connections.html

Only change on the client side is to add the following to ~/.ssh/config

# SSH over Session Manager
host i-* mi-*
    ProxyCommand sh -c "aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p'"

The ec2 plugin needs updating to allow instance id be an option in the Connection Strategy dropdown.