Eric, for different reasons unrelated to skiing, I had some pretty kinda sorta bad shoulder issues for awhile. In the end, I got things sorted out in the gym by weight training (dumbells) with relatively light weights while working through a large range of motion to strengthen the muscles around the rotator. It took a while, was painful at times, but am now pain free. Dumbells allow for a multitude of variations of twist, grip, angles, etc. for myself, I don't dally, and a 'set' isn't repeating the same lift for more than 12 reps rest, 12 more of the same etc... in the traditional way, but a series of different motions of 10-12 reps (one set of each) including flys, reverse flys, presses, etc... That make more of a circuit with very little rest between each movement variation. The idea was/is to work quickly and rigorously through a wide range of motion. Seems to have worked very well, and over the course of a year, was able to vastly improve overall shoulder strength and stability. Should help your water skiing too!
Of your pole plants are painful, I'd also try a set of adjustable poles like a Leki Vario and play a bit with length. Long poles can hurt. If you find yourself leaning on them a bit when making short turns, then you're probably a little back and in, though impossible to say without seeing you ski.