You ask the question 496 or 540. Those are to different blocks. I would be curious what you have to start with. That would dictate the basics of my build. You need a block with a 4.5" bore if you're going to build a 540. You can build about 500 ci out of a 454 block, but that's it. I believe in the saying, "There's no substitute for Cubic Inch." So build as big as you can with what you have. If money is no object, then go with a Dart block and build a sweet 540 that spins about 6000 rpm and makes 700 + H.P. all day long.
Frankly, this is the conversation you have with your builder, and from what I've heard Bostic would be an excellent choice. Then you come here and announce what you decided. As this thread has shown, the internet is full of opinions, and they're usually worth exactly what you paid for them.
Good Luck with the boat and the build.