Last summer I took NY Waterway's package "cruise" to Kyukit, the Rockefeller estate in Tarrytown, NY. It's an all day thing. You bring your lunch and NY Waterway (see link below) does the rest. I'd say for $60 it was an OK deal, but you don't get much garden out of it. We really enjoyed Philipsburg Manor, included in the tour -- it's a working 17th century colonial farm, and it has an interesting vegetable garden and a corn mill. (We made cornbread from the meal we bought there, and it was very tasty!) I think the two gardens I'd recommend you visit, along with the ones you mentioned, are the New York Botanical Garden and the gardens at the Cloisters (a branch of the Metropolitan Museum of Art). They're in the Bronx and very far northern Manhattan, in the vicinity of Wave Hill.
Have a wonderful trip!
Here is a link that might be useful: Tours on NY Waterway