I like 'em both...obviously.
Considering the NES and the Super NES have the same screen resolution (256 x 224), and that the original NES games had above-average graphics (at least in terms of detail), the upgrade was practically just more colour. It's certainly not as different, graphically, as the original Super Mario Bros. and its version in Super Mario All-Stars.
I like the music in both versions, but maybe I'm not as much of an audiophile as TerraEsperZ to notice if it was worse in the Super NES version (or maybe I have bad memory). I'd agree that I don't remember it being any better, if at all, but considering that I think the Ninja Gaiden games' soundtracks is among the best on the NES, I wouldn't have any bad words about the Super NES soundtrack.
I haven't played the recent Ninja Gaiden games, but I will say I prefer pyjamas-wearing Hayabusa over his now-visibly armored self. I dunno, I always seem to think that the armour makes him look less tough or something. I will still probably play those games at some point, as well as Ninja Gaiden: Dragon Sword (obviously for the DS, note the acronym of the subtitle) but somehow I doubt they will give me a nostalgic feeling like the kind I get when I look at these NES/Super NES maps.