Here's what we can say about the Magic that Colin Craven uses to account for both his and the Secret Garden's return to health: It's possibly the ghost of Lilias Craven, it's possibly God or what Mrs. Sowerby calls the "Good Big Thing" (26.63), and it's definitely the Force. Like the Force, the Magic draws together all living things; unlike the Force, sadly, the Magic doesn't give you any special advantage in lightsaber fighting.
When Colin first stands up, he thinks the Magic that is healing his legs is coming from Dickon, but Dickon tells him:
"Tha's doin' Magic thysel' […] It's same Magic as made these 'ere work out o' th' earth," and he touched with his thick boot a clump of crocuses in the grass. (22.10-12 )
See? Like we said: It's the Force, a.k.a. the good energy in the universe, that helps Colin stand and that brings plants out of the ground from seeds. And not only does it have these positive physical effects (healing neglected kids and producing green and growing things), but it also has a spiritual dimension as well. Dickon tells Mary privately that Mrs. Sowerby believes that the Magic in the garden is a maternal power coming from the lingering spirit of Lilias Craven:
"Mrs. Craven was a very lovely young lady," [Dickon] had gone on rather hesitatingly. "An' mother she thinks maybe she's about Misselthwaite many a time lookin' after Mester Colin, same as all mothers do when they're took out o' th' world. They have to come back, tha' sees. Happen she's been in the garden an' happen it was her set us to work, an' told us to bring him here." (21.31)
So the Magic is a combination of two central ideas in this novel: The importance of positive energy and thinking to a person's overall health, and the redeeming and healing power of motherly love. Lilias Craven, like Mrs. Sowerby, is a natural mother, so she has to keep watching over Colin even from beyond the grave. (We guess that Mrs. Lennox is just a failure all round.) With the help of his mother's ghostly spiritual power and the general happiness and good health of the Secret Garden, both Mary and Colin start thriving on Magic.