I suppose it is possible to argue that Milton's Paradise Lost is the greatest Protestant epic ever written. The reasons for this seem obvious to anyone reading it--the grandest theme possible, the sublime imagery, the baroque syntax (usually compared to Bach's organ music), the classical references, the eloquent speeches, and so on.
However--I would suggest Spenser's Faerie Queene might possibly be even better. Milton seems a bit cold and distant to me, and the sections of the poem dealing with God and Jesus just don't work. I don't buy the problem with Satan (that he is inadvertently the hero of the poem), but neither am I swayed emotionally by a lot of the rest of the poem. About the only part that really works for me is the before and after picture of Adam and Eve (I love the scene where the elephants entertain Adam and Eve).
In contrast, Spenser's poem seems much more alive. It is a wonderful straddling of Medieval allegory and Protestant emblemizing, and the raggedy, unique rhyme scheme is for me actually more engaging than the rather stiff stateliness of Milton's poem.
This certainly does not mean that Paradise Lost is not any good. I mean that, if I had a chance to read one or the other, I think I might grab Spenser. Readers today, especially Protestants who want to be culturally engaged beyond mere political involvement, ought to read in both works, every once in a while, every few years, making both of them part of the equipment of a well-stocked Christian mind.