FAO Schwatz is closer to the Zoo (if you haven't bought enough stuffed animals already!)

An alternative to the Zoo might be the Natural History Museum - just to have in your back pocket in case the weather is bad.

Out of Rockefeller and ESB I prefer the Rockefeller plus - it's a lot less hassle than the ESB plus you can see the ESB from it !

SI ferry is doable. each trip is about 30 mins but you have to get off and go around the landing area - you can't just stay on. I'd check the ferry schedule for actual timings. Personally I don't think you get that good a view of the SoL from it. You can see it but you don't get a close up view that you would from one of the tour boats. But kids seem to like being on a boat than seeing some "dumb statue" (as I head one American child call it).

The Roosevelt Island Tramway might appeal to your kids as an alternative to the SI Ferry. Has the advantage of being close to the zoo (about 5 blocks across and 3 down) and so making your trip a little more compact.