While they do take reservations on the Coupville-PT ferry, I've taken it without any. Last time the main deck was half empty. Think around local weekend travelers. Coming from the north I'd try to get a camping place on the island (midweek), possibly as the Fort Statepark right next to the ferry. Enjoy the night, watch the traffic, check with the ticket booth, and cross at your leasure the next day.
Occasionally ferry runs are canceled due to low tide. In the summer that's most likely to happen around noon around the biginning of the month. That's when the tidal range is greatest. But that's also the best time to walk the beach and tidal flats.
Another ferry option is the Edmonds/Kingston run. That's a bigger boat. Wait on Friday can be long when everyone in Seattle is heading out. It's also busy with the even rush hour.
For a double ferry run drive down Whidbey to Clinton, cross there, and back across at Edmonds.
Yet another option from Alaska is BC ferries to Vancouver Island, and Black Ball from Victoria to Port Angeles.