We've stayed several times at Sweetwater Forest cg in Brewster on the Cape. It's about mid-Cape and yes the traffic to Provincetown can be a slow crawl.
If you camp on the Cape take your bikes - the Rail Trail is a nice, easy paved multi-use trail. DW & I enjoyed the Cape Cod Museum of Natural History, the National Seashore Salt Marsh Visitor Center (interesting canoe trips), biking to the beach, and the rather interesting sights in Provincetown.
We did a day trip to the Whaling Museum in New Bedford but were rather disappointed in it. Both of us much preferred the private museum in Nantucket (but the ferry will cost you $$$.)
Brewster also has the General Store and an ice creme shop next to it. And either while biking or driving you should stop at Arnold's for a meal or snack.
We've done several whale watching trips from various ports including Provincetown. Nice, but now the novelty's worn off for us. Last summer I paid the $50 for a 7-day pass to drive on Race Point beach. Pack the cabanna & cooler, drive out on the sand, pull up a piece of beach, and relax for most of the day.
We used to stay at a cg in Gloucester, take the train to North Station, and hoof it around Boston. We took a Duck Boat tour and had a really humorous and informative driver / guide. You can do all or part of the Freedom Trail there. And do try one of the many family-owned restaurants in the North End.
If we were to go back to Boston itself I'd be giving Minuteman cg a try.