I.N.
You just have to make sure your little one doesn't go too far in! That and use plenty of sunscreen. Oh, and my kids seem to attract a lot of sand spurs. And my youngest complained about the shells in the waves hurting her feet- we solved that one with beach shoes. Also, it helps to have a bathroom nearby. I like taking my kids to the aquarium- either at Ft. Fisher or in Manteo. But my kids have a great time just playing in the water and building sand castles. Boats are always neat, too, so you could go to the battleship in Wilmington.
A lot of rental companies have weekend deals for the fall. When I look, I just google "Wrightsville Beach rentals" or whatever beach you want to go to. I've always stayed at houses at the beach instead of hotels, so I can't help you with that, but I have seen ads in the Sunday paper for weekend beach packages at hotels.
Remember that your son will still get REALLY tired, so it may be best to not plan much, but just go with the flow. I do one activity a day with my kids when we're there; otherwise they get crabby and ruin MY fun! Have a great time!!!