Hi zandemom,
Sounds like an interesting project for a third grader! However, I just wanted to point out a couple of aspects that might complicate the project. First, it involves a bit of physics because if you're throwing each ball, you're creating projectiles, like so:
http://library.thinkquest.org/06aug/022 ... age005.gif. You're also starting with a velocity that's not zero meters/second, so that too is a variable. Additionally, because each ball is made of different materials (regardless of weight), that's another independent variable. Therefore, if you want to focus on weight alone, you could try to find footballs of the same material but different weights. As for the initial velocity of the ball, I wouldn't worry too much about it if your son throws in a constant and consistent nature each time. Besides, it's ridiculous what football launching machines cost!
Because this is the third grade level, explanations for hypotheses can be and usually are on an intuitive level, i.e. The heavier balls in general will not go farther because they will fall faster than the lighter balls. Of course, the actual reason you give is up to you. Also recall that a hypothesis is pretty much an educated guess at what will happen. It can be supported, refuted, or qualified by the results, so even if the results contradict the hypothesis, that's perfectly fine! Your son will just need to understand why that was so through his own explanation, something appropriate for his grade level.
Hope this helps and good luck!