Executing a command using Net::SSH
In my opinion, your method does not have too many lines, but the line calling Net::SSH.start is too long. 

My terminals and text editors are 80 characters wide, so I would split the long line into 2 lines

      Net::SSH.start(@tunnel_ip, @tunnel_username, keys: @tunnel_key_name,
                     verify_host_key: false) do |ssh|


If you must reduce the number of lines, you can move some lines into new methods. The extra method calls will make spaghetti of the control flow, so the code will be difficult to read and understand, but it might satisfy your cop.

    def tunnel_run(cmd)
        retries = 0
        code = tunnel_run_command(cmd)
        abort ... if code != 0
    rescue Net::SSH::ConnectionTimeout
        ...
    end

    private
    def tunnel_run_command(cmd)
        code = nil
        Net::SSH.start(...) do |ssh|
            the_channel = ssh.open_channel do |channel|
                channel.exec do |ch, success|
                    code = tunnel_run_channel(ch, success)
                end
            end
            the_channel.wait
        end
        code
    end

    def tunnel_run_channel(ch, success)
        code = nil
        raise ... unless success
        ch.on_data { ... }
        ch.on_extended_data { ... }
        ch.on_request("exit-status") { ... }
        code
    end


Beware that the private methods tunnel_run_command and tunnel_run_channel will pollute the method namespace in all objects that extend Tunnelable.  Privacy in Ruby is by object, so the object inherits the private methods from Tunnelable, and Ruby allows the object to call those methods. 

The names tunnel_run_command and tunnel_run_channel must not conflict with other methods of the object.