The ferry terminals at Highlands & Atlantic Highlands (http://www.seastreak.com) and Belford/Middletown (New York Waterway http://www.nywaterway.com) all provide parking to passengers as part of the ticket.
Parking at New Jersey Transit stations varies... your best bet is to check out their website (http://www.njtransit.com/rg/rg_servlet.srv?hdnPageAction=TrainStationLookupTo) for specific information including rates for the stations that are of interest to you.
Hope that helps!
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