I would also ask what sort of materials are you considering and what general type of boat?
If you are considering wooden boats, Chesapeake Light Craft makes a variety of very attractive plywood kit boats that are well thought out and produce very nice boats. http://www.clcboats.com/
If you are considering a sailboat, there are some older style one design classes like the Penguin, Mirror and Enterprise dinghies which are easy to build and produce nice boats for a 13 year old. Depending on where you live, Penguins are still popular and the wooden ones are still competitive and marketable. There is info on the Penguins at http://home.dmv.com/~jenkins/
I would think that your son would quickly out grow something like an Optimist Pram (Opti),Sabot or El Toro dinghy which are used for the most basic level Jr. Trainers.
There are also a number of websites that have old wooden boat designs that have fallen into the public domain. While the designs are free, most are very dated and many were not very good designs to begin with. One of the bigger free plans sites is Svensens. http://www.svensons.com/boat/
I think that there are few father-son projects that can compare with working on a boat in terms of creating a bond between a parent to a child. My father and I started working on my family''s boats when I was just slightly younger than your son, and it created a close friendship that endures to this day and certainly took the edges off of going through my teenage years.