If your pulling it from the top, I would say remove the plenum. It gives you better access to the rear of the engine, and the trans bolts. It also gives you more options as far as attaching a chain and lifting the engine out.
However, if your dropping the engine/cradle assembly out the bottom of the car, then leave the plenum attached. With the whole front end sitting on the floor, engine, trans, and all, everything is accessible.