both have their place and use. both are good.
(most) long-arm quilters use polyester thread for quilting...it is strong, there are lots of colors, it is inexpensive.
cotton thread is used by many...hand quilters use cotton thread alot (cotton thread does not work for long-arm quilting- it breaks every few inches.) for piecing i use what ever works at the moment...cotton/poly blends, rayon, poly, silk, nylon and monofilament.
use what works for you.
for hand piecing and applique i use silk thread. for machine work usually a blend. i seldom use cotton thread i am too impatient to put up with the constant breakage/rethreading.