I don’t think there is any “best” technique for water. It depends on how much time and effort you’re willing to put into your movie.  I have seen lots of different ways to do it and each one works in the animation.

I just recently watched The Lego Kraken (so it is the most fresh in my mind) and I enjoyed the use of 1x1 plates to simulate movement around boats and the monster itself. The small bricks themselves were different colors that helped sell the effect. Another film that uses the small blue bricks to good use (with a small brick built water effect too) is Stranger than Fishin. Mindgame also uses blue paper with small movements for a subtle effect. I believe both films did a great job of simulating water with minimal bricks.

I remember other animations where the surf meets the shore (with white mixed in for foam) but I don’t remember which movie it was. These used bigger bricks and pulled up on the shore and receded. If you’re looking to make realistic movements you might go to a lake and observe the movement of water when you do different things.

Clay might be nice if you’d like to make realistic splashes or have water froth and foam. I don’t know much about making water in post production-I just think it would be harder as defining where the water should be in each frame might be different. But don’t let my words stop you-you probably know more about this than me.

If making water digitally or in the shot seems complicated you might try focusing on the boat and have no water in the shot. Just make sure to make your boat SEEM like it’s on the water with a little rolling, rising and sliding along.
Have fun,
Jared