If you WANT to use your way and loading this datasource "by hand" and not like Matt said, you would initiate it like this:
# /path/to/your/datasource
class MongoDbDatasource {...} //check how this class is named!
Within your file where you load it you can do this:
App::uses( MongodbSource , Mongodb.Model/Datasource );
$mongodb = new MongoDbDatasource();
But as said, the databsae configuration would be the better way:
public $default = array(
datasource => Mongodb.MongodbSource ,
database => mydbname ,
host => yourhost ,
port => yourport ,
login => yourlogin ,
password => yourpassword
);
Now you just have so add CakePlugin::load( Mongodb );
to your bootstrap.php
so your plugin will be loaded.