I've been considering landing gear on my latest big build cruiser as well, actually.
What I've come up with is the retractable landing gear with the docker on the belly of the ship. I'll then dock it using pickup rails.
That way I can have the docker be in the middle or even back of the ship that can dock onto a physical rail and then slide forwards onto the intangible pickup rail, then use logic to sense that the ship is docked to trigger the landing gear to extend.
In theory it should make it look as though the ship is coming in and slowly hovering into position while it's landing gear extend.