LP, you're here at the best time!
If I were you I'd head to the Lower/Outer Cape and spend some time in the National Seashore. There's some gorgeous trails, mostly pretty flat, so easy to handle with the wee one. If you like biking, you can rent a bike with a kiddie carrier and cycle the Rail Trail. Head to Provincetown for walks and bikes through the woods and dunes; you can actually get chicadees to feed from your hand in the Beech Forest! Take a walk along the pier to look at the boats - pretty cool if you can ignore the fact that they're - you know - fishing boats :/
Depending how early you're here, my workplace (Center for Coastal Studies in Provincetown) has some fun activities - the tidal pool explorations are popular! Check out our website or FB page for info closer to the time (www.coastalstudies.org
The Natural History Museum on 6A in Brewster has a great collection of aquariums and also a few reptiles, and a touch tank with local critters.
In Chatham, the Fish Pier usually has a couple of seals hanging around the harbor, they're so flippin cute. Best time to see them is when the day boats come back, they love a snack or 8 from the fishermen.
At the other end of the Cape, there's a cool Children's Museum in Mashpee that has loads of fun activities.
Have you been to Nantucket? You can get the ferry over either from Hyannis or Harwich, everything is within walking distance when you get there. There's also the Cape Cod Maritime Museum which has a kiddie area and a wooden boatbuilding shop.
Re. food - if you're in W Yarmouth you're only a few miles from Trader Joes (Next to the Mall in Hyannis) and there's a Stop and Shop close by too. S and S is doing a much better job for vegans these days :)
If I think of anything else I'll come and post... Happy Planning!!!