"Erase all map data" deletes and replaces the map with a new map, just like creating a 'New Blank Map'.

"Erase tile data + doors + NPC instances" deletes the map layers, wallmap, foemap, doors, and NPC instances. It leaves the NPC definitions and General Map Data intact. This is useful when used on copied maps.

"Erase NPC instances" deletes all NPCs placed on the map, but not any NPC definitions.
Notice that you can delete all copies of a specific NPC by pressing DELETE while in the "Edit NPCs" menu.

Other options are self-explanatory.

If this map is the last map, an additional option appears, "Delete map entirely".