I've been to both. El Salvador> Pro's: If you're driving, the roads are much nicer, basically all right hand point breaks, we found more non-surfing activities to do and slightly less crowded. Con's: A bit more agro in the line-up, sketchier characters outside the line-up (if you're halfway smart about it you should be alright), basically all right hand point breaks and a better chance of getting sick from polluted water. Nicaragua> Pro's: All day offshore's, mellower line-ups, a bit cleaner, almost 100% chance of getting barreled and we felt a little safer. Con's: Crowded line-ups, horrible roads, less non-surfing activities and jelly fish for days (at least when I was there)
For reference, in Nicaragua we stayed at Iguana Beach and surfed there most the time. I would highly recommend it. In El Salvador we stayed in El Zonte and surfed there plenty but also got out and sampled a lot of other waves.
If I had to choose between the two again I'd definitely lean towards Nicaragua.