We go to the cape every year, but always in off season. When are you planning on going?
The beach will keep the little one entertained for hours. Bring along a few pails and shovels. You can walk along and collect treasures, build sand castles, or swim.
The Kennedy Memorial is a great spot to have a picnic lunch, with tables in the shade. There's a small playground, however, it's geared toward older kids. There's also a small beach area, and in low tide you can see small water creatures like crabs and little fish. The bathrooms have always been clean.
I haven't been in almost 10 years and didn't have a good experience, but there's the Zooquarium in Yarmouth. You could check on-line opinion sites to see if it's been upgraded.
I don't recommend a whale watch for a 3 year old. IMO it's just too young, you'll spend too much time worrying about his safety. Also, a big part of going on a whale watch is learning about the whales, not just viewing.
You'll find several mini-golf courses.
There's a pirate adventure, where you go out on a boat. I'll see if I can find the exact name for you. I've never been, but have heard it's great.
