Ok, I've been trying some more stuff here and there and having some thoughts here and there. Saddly, not all of it worked...

First I changed the walls from Surface Cyls, to Surface Plains and the particle flow stayed inside. But still having collision problems between the boat and particles.
Next I had a thought on putting pieces of "Pond Blocks" so the particles are effects and the motion is done through boat, but I couldn't really combine the Gravity Rigid Body with the Boat Locator. So next I thought of maybe having "Fluid Blocks" and add Fluid Collide. Trouble there is that Maya crashes as soon as the boat enters the fluid (boundaries).
So I have one final thought here. Is there any way one can have Soft Collisions on Particles? As particle collisions go now if one particle hits the boat the boat jumps, and if the boat falls in a river of them it gets shot off in some direction. Wondering if there's some way to like do so that the particles are not rock hard but either air or water soft. Or alternatively help me with some scripting so that if the distance between a particle and the boat is below something, move the boat (under rigid body properties) in the direction of that particle.

/Edward