I guess it depends where you're shooting from mainly too as to what your best lens choice will be. Do you plan on a chase boat or just shoot from the pull boat?
I was waiting for somebody to ask this question. Very important.
TO be in the pull boat, a 70-200 is good, to be on the shore somewhere else, you will need a long lens!
You cannot get the DOF on a F4 as you woudl on a 2.8. You won't need the speed of the 2.8 on 95% of the days, but the DOF is something you might consider. If you can't get the L lens (canon), try Sigma or some other third party. Image quality might not be the best, but it'll save you money and depending on quality, might be just fine for your use.
As for body's, I own an XTi and a 40D. The XTi works great in well lit situation, and can be had cheap used. The downside? Low light conditions, and speed if you use continuous. I shoot sports and never use continuous so it's not a problem. The 40D's technology allows for the picture to be pushed a lot more in PP then the Xti, but some of my best work was captured with the Xti. If you are looking to save money, and plan on shooting well lite days, I'd suggest the XTi.
I'm not as familiar with Nikon, but my buddy has a D80, and D200. Both great cameras as well. D80 is about the same cost as the Xti, and D200's are dropping in price FAST! Another solid body. Nikon's body's feel great, but I love my Canon. I love Canon lenses.