Not much of a difference really apart from having to take into consideration slight design alterations so you don't get a hundred arrows in your face.
They both drop the same amount of XP (5). There is more of a market for bones and arrows than there is for rotten flesh. So skeleton would be better if you had to choose between the two.
I would want to go with the zombie spawner because there is a design for a AUTOMATIC xp farm by xisumavoid right here ---> #mce_temp_url#.