Start with something most guides will not tell you: Cape Cod has a small guided-tour market, and that is not a failing. This is a destination you do yourself. You drive the 6A, you walk out on the flats, you ride the rail trail, you find a pond. The number of experiences you can actually book here runs to a few dozen rather than a few hundred, and a page pretending otherwise would be padding.
What that small market does have is one genuinely excellent vertical. Whale watching out of Provincetown and Barnstable is not a novelty ride; it is a trip to a federally designated marine sanctuary where large whales feed in numbers, run by crews who have been doing it for decades and who often carry naturalists collecting real data. If you book one thing on the Cape, book that.
Around it sits a second tier that is thin but real. Seal cruises from Chatham and Harwich into the Monomoy shoals. Four-wheel-drive dune tours over the Province Lands, which is the only legal way into that landscape. Guided kayak trips on the salt marshes and estuaries. Sport fishing charters, inshore for striped bass and bluefish or further out for tuna and shark. Sunset sails on Cape Cod Bay. A handful of walking and food tours in the bigger towns, and trolley sightseeing in Provincetown and Hyannis.
And then there is a third category worth naming clearly, because visitors waste money on it: things that are sold as tours and are better done unguided. Lighthouse tours are a drive you can do yourself with this site open in the passenger seat. Rail trail tours are a bicycle. Beach tours are a car park and a staircase. The islands are reached by scheduled ferry, and a ferry is transport, not an excursion, though plenty of packages will happily sell it to you as one.
Two structural facts shape all of it. First, the season: outside roughly mid-April to late October, most of this simply does not run. Whale boats start in spring and stop in autumn, dune operators and seal cruises work the warm months, and the winter Cape has almost nothing bookable on the water at all. Second, the weather cancels things. Massachusetts Bay gets rough, fog forms fast over cold water with a southwest wind, and a small-boat trip is at the mercy of both. Book the thing you care about early in your stay so there is somewhere to move it to, and take the first sailing of the day whenever the choice exists.
What follows is sorted by depth of market, most substantial first, with an honest note on each about who it suits and when it is worth skipping.