Start with an honest measurement. Cape Cod has a small bookable boat market, smaller than almost anywhere else with this much coastline, and a visitor who arrives expecting the Florida model of a dozen operators competing on a dock will be surprised. Some of that is regulatory, some of it is the sharp season, and a lot of it is that the peninsula's boating culture is private rather than commercial: there are more moorings per head here than almost anywhere in New England, and most of them belong to somebody who does not want your business.
What exists, and is worth booking, falls into four groups. Whale watching out of Provincetown and Barnstable is the deep end of the market and has its own page. Seal trips out of Chatham are the other wildlife vertical. Then there are the harbour cruises and sailing trips, which are the subject of this page: a schooner working Provincetown Harbor under sail, sunset trips out of Hyannis past a stretch of shoreline you cannot see from any road, charter sails on Vineyard Sound out of Falmouth and Woods Hole, and the small shuttle across Provincetown Harbor to Long Point, which is transport rather than sightseeing and is one of the best half-hours on the Cape. Fishing charters are a genuine fifth, covered separately.
Two things shape every booking here and neither is obvious. The first is the tide. Several of the Cape's harbours sit on the bay side, where the range runs to nine or ten feet and the basins empty almost completely at low water. Rock Harbor in Orleans is the clearest example: a working sportfishing harbour whose channel across the flats is marked by a line of spruce trunks stuck in the mud, and whose fleet can only come and go around high water. When an operator offers you a departure at ten past seven in the morning, that is the tide rather than a preference.
The second is the calendar. Almost nothing on this list runs between Columbus Day and Memorial Day. Boats come out of the water, crews go elsewhere, and a harbour that had four operators in August has none in February. If you are here in the shoulder, ring before you drive.
One more thing that makes Cape Cod boating unlike a resort coast: the Cape Cod Canal. Seven and a half miles of sea-level channel cut across the base of the peninsula, wide, deep, free to transit and actively controlled by the Army Corps of Engineers, with a current that reverses and runs hard. It is a working waterway rather than an attraction, and seeing it from a boat rather than from the bike path beside it changes what you understand about the place.