Can't speak for yoga much -- except my HS and college wrestling coaches were both big believers. But that was years ago. But I know that Pilates is da bomb in terms of building core strength, balance, and flexibility. Just as there must be sports specific Yoga routines that one can add to one's work out, there are definitely sports specific Pilates routines. Pilates has a great set of exercises that work on the obliques for example -- and every baseball player needs strong and flexible obliques.
Main difference between Pilates and Yoga, as I understand it, is that Pilates is more "dynamic" but otherwise they are very similar I think.