Yeah, what Matt said. Start out at the info sites and you should be able to see what you're missing. Dallas Vintage Toys has several WHALE parts for a good price, (they have 12 or so different pieces around 3/4 of the way down on the 1st page)
http://www.dallasvintagetoys.com/vehicleparts.aspx
And ebay has a ton scattered all over the place on price/shipping. But if you can find several from the same seller, then shipping on stuff that light shouldn't be bad to combine.
http://www.ebay.com/sch/i.html?_from=R40&_trksid=m570.l1313&_nkw=gi+joe+whale+parts&_sacat=0
Kudos to your son for picking out such a cool freaking toy! I didn't really have any of the "big" vehicles from the Joe line when I was a kid, but I did get the WHALE. It was my favorite vehicle then and still is today. The depth charges and little motorcycle thing and the awesome rotating gun turrets... ah, memories.