I'll demonstrate the lack of an isomorphism via a counterexample.

Consider MaybeT and WriterT (and the basic Identity monad for the bottom of our stack)

    newtype MaybeT    m a = MaybeT   { runMaybeT   :: m (Maybe a) }
    newtype WriterT w m a = WriterT  { runWriterT  :: m (a, w)    }
    newtype Identity    a = Identity { runIdentity :: a           }

I'm going to claim that MaybeT (WriterT w Identity) is not isomorphic to WriterT w (MaybeT Identity). If we expand the first

    MaybeT (WriterT w Identity) a
    ==
    WriterT w Identity (Maybe a)
    ==
    Identity (Maybe a, w)
    ==
    (Maybe a, w)

And if we expand the second

    WriterT w (MaybeT Identity) a
    ==
    MaybeT Identity (a, w)
    ==
    Identity (Maybe (a, w))
    ==
    Maybe (a, w)

So we can see that the Maybe is wrapped around something different in each stack. So now to the claim that there's no isomorphism should be obvious---any witnesses to the isomorphism f and g would have to have that for all w, f (g (Nothing, w)) = (Nothing, w), but since g :: (Maybe a, w) -> Maybe (a, w) cannot fabricate an `a`, it must be such that g (Nothing, w) = Nothing which means that f :: Maybe (a, w) -> (Maybe a, w) cannot determine the right `w` to return.