This thread is a bit old, but since I've spent a frustrating afternoon discovering a simple solution, I might as well share it.

NB This is not a strict answer to the OP's question, as it doesn't use ssh. But, one point of boto3 is that you don't have to - so I think in most circumstances this would be the preferred way of achieving the OP's goal, as s/he can use his/her existing boto3 configuration trivially.

AWS' Run Command is built into botocore (so this should apply to both boto and boto3, as far as I know) but disclaimer: I've only tested this with boto3.

def execute_commands_on_linux_instances(client, commands, instance_ids):
    """Runs commands on remote linux instances
    :param client: a boto/boto3 ssm client
    :param commands: a list of strings, each one a command to execute on the instances
    :param instance_ids: a list of instance_id strings, of the instances on which to execute the command
    :return: the response from the send_command function (check the boto3 docs for ssm client.send_command() )
    """

    resp = client.send_command(
        DocumentName="AWS-RunShellScript", # One of AWS' preconfigured documents
        Parameters={'commands': commands},
        InstanceIds=instance_ids,
    )
    return resp

# Example use:
ssm_client = boto3.client('ssm') # Need your credentials here
commands = ['echo "hello world"']
instance_ids = ['an_instance_id_string']
execute_commands_on_linux_instances(ssm_client, commands, instance_ids)

For windows instance powershell commands you'd use an alternative option:

        DocumentName="AWS-RunPowerShellScript",

You can use the following code snippet to ssh to an EC2 instance and run some command from boto3.

import boto3
import botocore
import paramiko

key = paramiko.RSAKey.from_private_key_file(path/to/mykey.pem)
client = paramiko.SSHClient()
client.set_missing_host_key_policy(paramiko.AutoAddPolicy())

# Connect/ssh to an instance
try:
    # Here 'ubuntu' is user name and 'instance_ip' is public IP of EC2
    client.connect(hostname=instance_ip, username="ubuntu", pkey=key)

    # Execute a command(cmd) after connecting/ssh to an instance
    stdin, stdout, stderr = client.exec_command(cmd)
    print stdout.read()

    # close the client connection once the job is done
    client.close()
    break

except Exception, e:
    print e

Here is how I have done

import boto3
import botocore
import boto
import paramiko

ec2 = boto3.resource('ec2')

instances = ec2.instances.filter(
    Filters=[{'Name': 'instance-state-name', 'Values': ['running']}])
i = 0
for instance in instances:
    print(instance.id, instance.instance_type)
    i+= 1
x = int(input("Enter your choice: "))
try:
    ssh = paramiko.SSHClient()
    ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
    privkey = paramiko.RSAKey.from_private_key_file('address to .pem key')
    ssh.connect(instance.public_dns_name,username='ec2-user',pkey=privkey)
    stdin, stdout, stderr = ssh.exec_command('python input_x.py')
    stdin.flush()
    data = stdout.read().splitlines()
    for line in data:
        x = line.decode()
        #print(line.decode())
        print(x,i)
        ssh.close()

For the credentails, I have added AWSCLI package, then in the terminal run

aws configure

enter the credentials. All of them will be saved in .aws folder, u can change the path too.