In general waterjet will hold better tolerances and make a nicer finish than plasma. For thin material it may not matter. But when you get in to very thick material waterjet will definitely be the way to go. Waterjets can basically handle any thickness material just by altering their feed rate. With plasma as you go thicker you need a bigger and bigger machine. Almost any waterjet can cut 5"+ thick material. There are multi-axis waterjets that will account for taper of the jet as well.
You can learn about waterjet cutting at:
http://waterjets.org/ (not affiliated)