If it's an outboard disconnect from the main tank and run it on a small portable tank with good gasoline.
Try and find out if the tank in the boat is a steel or aluminium tank. If steel you are going to have rust issues, and replacement is about the only option at that point. You can get a matching tank thru West Marine's website pretty easily.
As for emptying the tank, disconnect the fuel lane between the fuel pump and carb and run the hose into a drain tank or bucket, let the battery pump it out. Another option is to take the fuel line directly off the tank fitting and siphon from there.
A good idea would be, once you get all that stuff out, to put an inline fuel filter into the line before the fuel pump. They have quick-change types and water separators that are inexpensive and easy to mount. Mine cost 32$ and catches an amazing amount of crud.