Which works better?

DOSBOX. Stuff like fast menu animations are minor stuff and even more acceptable for people who never liked their laziness. Also in DOSBOX hitboxes and reactions you vs enemies are faster + more accurate. In DOSBOX it was easy to beat Moon, in SWPORT my units were lazy, barely accurate and enemies had too much defense to actually damage them more than they do stuff to me (so I didn't have famous speed bug but SWPORT interaction compared to pixel-to-pixel perfection I got in DOSBOX was beyond comfortable). Also no music change in-mission and no music in Orbital Station (there WAS music in original not just background ambient). Both version share bug related to Orbital Station (explosives can't be pickuped sometimes so this will go boom an level fail).

SWPORT has their on merits and pace, DOSBOX is close to resonance your mind cycles to cycles in game. ;-P