If you can, I would get both. You can save some money by going to a gaming store and buy a used version (not to mention the fact you might get lucky and get some pretty good Pokes - I got a Lv13 Celebi from my used Ruby version) of each.
But if it HAS to be one or the other, I would definitely suggest Emerald. FireRed is nice, but Emerald is hands down the best (advanced gen) game on the market. The playability and the breeding aspects, not to mention the wicked awesome Battle Frontier, are well worth it. While you won't get the Legendary Birds or Mewtwo, you do get all 3 Hoenn Legendaries and you can even choose which Lati@s you want to catch. That in of itself is awesome, especially since you already have Ruby.