Hmmm. Tough call!
From the top view, the "smoothed delta, nacelles back" has a nice look to it. I also like the similar underside view. It gives the ship a very sleek, sweeping look to it.
But from the profile, nacelle's swept down seem like they are below the ship's center of gravity, which makes me inclined to vote nacelles up. I don't know if\how this applies to ST engine design--warbirds and bird-of-prey are built that way, aren't they?--but I'd think the lower Nacelles would make the ship nose-heavy. Of course, that could be a good plot point if you were using it in a story!
