"This was the tree, and it seemed to me standing there to resemble those men, the giants of your childhood, whom you encounter years later and find that they are not merely smaller in relation to your growth..."
This is figurative because the tree is being used as a metaphor for how children perceive adults, and how adults look back on their childhood. Things that seemed so large/important then seem to shrink with age.
"The tree tremendous, an irate, steely black steeple beside the river."
Here, the same tree is being compared to a "steeple", as in a church steeple, giving it a religious and more important significance.
"The beach shed its deadness...and finally it was totally white and stainless, as pure as the shores of Eden. Phineas, still asleep...made me think of Lazarus, brought back to life by the touch of God."
Here, there are two allusions to the Bible in how Gene describes Finny.
"[Up above] the cold Yankee stars ruled this night. They did not invoke in me thoughts of God, or sailing before the mast, or some great love as crowded night skies at home had done...."
The stars have multiple meanings - they could bring thoughts of heaven or of celestial navigation, but instead for Gene they indicate his feeling of insignificance in the universe.
"The early snow was commandeered as its advance guard."
The snow is metaphorically described in terms of war, which was on the minds of all the students.