Working with MongoDB in CodeIgniter wouldn't be much different than working with it anywhere else.
You could knock together a MongoDB library that would connect in the constructor and store $this->conn to be used in methods later on.
then either work directly with the conn property in your controllers or create a few methods in your MongoDB library to do this for you.
Take a look here to see the plain PHP tutorial for working with MongoDB.
I'd happily create you a library for this but it would come with a price. :-p
