Estoc has a nice reach but rapier seems to get a slight critical bonus, not as large as Bandit's Dagger though.
Alternately, could make either of said weapons a normal +15 and use CMW on them, but got no idea how long the buff lasts, so for easiness of use in mind, wouldn't it be better to just magic upgrade one or the other? --- If the above post offended you, chances are you needed to be offended.
I think it depends on what your playstyle is like. If you're adept at backstabs/ripostes you probably want to go with a Magic (or Enchanted) rapier, as I hear it does more BS damage than estoc. If you want to slug it out, a CMW estoc does a lot of damage per poke.
Depends. Enchanted will outdamage magic on an INT build. Enchanted estoc +5 has "B" INT scaling. I think an enchanted rapier does as well. A +5 enchanted Balder side sword goes to "A" scaling. I carry an enchanted weapon for general use and a +15 Uchigatana for when I want to use CMW.