The first quatrain tells us that the poet, Johnson, has lost his son at seven years old. Johnson’s son died of the plague. The narrator opens the poem with an apostrophe which is when the speaker speaks directly to an imaginary person or abstract idea. Here, “Farewell,” indicates that he is speaking to his son, perhaps at his gravestone, or just to his spirit.
Beginning with “Oh, could I lose all father now” – this is ambiguous or it simply has a double or triple meaning. This could be the poet saying he’s about to emotionally lose it, grief-stricken. And/or it means that the poet is losing his child and the child is losing his father. And/or the child is speaking (or the poet imagines this) and the child says he is losing his life and escaping from the “world’s and flesh’s rage,” which is of some comfort to both father and son because the son is not physically suffering anymore.
“Here doth lie Ben Johnson his best piece of poetry.” Note that it does not say Ben Johnson’s, so here could also be a double-meaning. One meaning is that his son is his best creation; his best poetry. The second meaning is that Ben Johnson lies in the grave as well. Interpret this how you wish: part of him died when his son did, they are blood-related so physically as well as spiritually connected and Johnson (the poet/narrator) will never forget his son, his best creation. Therefore, all his poetry and all his best creation will be for his son; a lasting tribute and to keep his memory alive. “For whose sake henceforth all his vows be such.”