We've been to the Cape a few times and have always stayed at Sweetwater Forest in Brewster.
Yes, traffic is horrendous in the summer, especially going all the way to Provincetown (P-town.)
Do bring your bikes, the Cape Cod Rail Trail is a paved multi-use trail following an old railroad bed. The busiest road crossings have an over- or underpass for the crossing. We've also parked at the Salt Marsh visitor center and biked to the beach.
If you have a 4X4, proper size tires, and a few other odds and ends you can get a permit ($50 / week) to drive on the beach. We'd head out, pack the cabana and lunch, pull up a piece of sand, and spend the day.
If you're interested in whaling history, the private museum on Nantucket is better than the NPS one in New Bedford IMHO.
You should visit the Brewster General Store and have some ice cream next door.
We've done several whale watching trips, interesting the first few times but now it's gotten old for us.