I prefer poly. I handquilt and tie a lot and it works the best - the needle goes through easily and doesn't have to be tied so close. And it is lightweight and has more loft. Cotton in a large quilt gets heavy, IMO. I have done a little machine quilting with poly and it was fine.
Whatever you decide to use, if you are tying, make sure it is not a batting that has to be quilted 2 to 4" apart.