Castlevania III is the best game on the NES, period. 4 characters, all of whom are interesting and fun in their own ways. Very good level design (although I won't defend level 9...) and multiple paths. Quite hard, through legitimate challenge rather than bad design. And I don't think I need to comment on the music!
IV is very close behind in my mind - I think III is the stronger all-around game by a hair. I'd probably give the nod to IV if it had the multiple characters and/or paths.
X68000 would be my 3rd...I've never played Chronicles but have beaten the original version. That is exactly how you do a remake!
SOTN isn't quite my style of game but I still enjoyed it a lot and would have no problem with anyone saying it's the best.