I would say most tourist attraction type boats are wheelchair accessible. The cruises around the Bay in Seattle are easy and fun.

 

Lake or river boats can be a challenge depending on the water level. The higher the water level, the steeper the ramp is on the dock to get to the boat. 

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One year we went to San Francisco and took a boat ride over to Alcatraz. The type of vessel to get there was a larger speedboat. It was windy that day and very choppy waters. My advice is to stay near the middle of the boat and make sure you have a friend hanging on with you.

 

As far as ferries go, I have not come across one in the United States that is not wheelchair accessible or doesn't have dedicated seating for wheelchairs.