It's cheaper if you can DIY repair and you can get Xperia Z3 replacement parts here http://www.witrigs.com/replacement-parts-for-sony-xperia-z3
But the disadvantage is that you can't ensure the phone still waterproof. So i think the reason why cost so much to Sony Service center is that they can give you the promise that your phone still be waterproof.
So you need to make a decision.