The Force is an energy field that is created by, and flows through, all living things. It permeates the Galaxy, even on dead planets, around inanimate objects, and in the near-vacuum of space where there are no living things, and it binds everything together.
Midi-chlorians allow Force practitioners to communicate with the Force and manipulate it (or rather the Force communicates through midi-chlorians if its practitioners are skilled enough to 'hear' it). The Living Force channels energy from all living things, and feeds it into the Cosmic Force which binds everything together, hence why the Force is all around them.
Although the Force is created by living things, that doesn't mean it can only affect living things or can only work in the presence of living things other than the people using it. Force practitioners can use the Force:
- in the near-vacuum of space on a spaceship, such as Darth Vader remote force-choking his subordinates over the holocom
- over great distances, for instance Force telepathy had no distance limit where a link existed between the two practitioners, such as brother and sister
- even where there is very little life other than themselves such as on dead planets or indeed in and inbetween space
- as is often exemplified, on inanimate objects such as ships or rocks
In addition, because the Force is living, it can communicate knowledge about itself even at a distance, for instance when Obi-wan feels the destruction of Alderaan, or in this case when Yoda needs to manipulate it around the ship.
In TESB, when Yoda is instructing Luke and lifts his ship out of the swamp, he is not communicating with midi-chlorians in the ship or around the ship, he is using his own midi-chlorians to communicate with this energy field, which is flowing around the ship and between himself and the ship, so that he can focus on moving the ship by manipulating the energy field around it.
It is this energy, from all of the living things on the planet, and all the living things in the galaxy, which binds everything together, which is what is between Luke, Yoda, the tree, the rock.