I've never heard of the Brooklyn Ice Cream Factory, so I have no idea what the draw is there?
Dylan's is an overpriced, tourist-packed candy store. I'd not go near it if I were you. She's got a good pr budget.
We have an aquarium? For serious?
Things not on your list you may be interested in - by Grant's Tomb (which is cool to say you've gone and it's a neat building and he's indeed there but it's not a big attraction, it's one building), there's Riverside Church and, better, since you can't climb up in their bell tower anymore, St. John's Cathedral. It's the largest cathedral in like, the world, or some such - it's very, very impressive. Huge, gorgeous, different chapels, massive stained glass windows, lot of history, and a cool garden with wandering peacocks.
Also right in between Grant's Tomb and the Cathedral is Columbia University. I highly recommend visiting the campus. It's open to just walk onto. It's a total departure - you walk off Broadway through a little gate into an entirely different world. It's a massive campus of old, classic buildings, huge expanses of grass, trees, it's lovely and amazing. If you go on the right day, you can also catch an astronomy lecture (open to the public, geared toward the layperson and attract tons of kids -
info and schedule here ) and afterwards, go up to the roof of the astronomy building and use the observatory telescopes.
Up that way, past Grant's Tomb, but an easy bus ride (the regular city bus), is the Cloisters - a branch of the Met Museum dedicated to Medieval art, archietcture, literature, etc. located in a castle in Ft. Tryon Park. Has amazing views of the Hudson, lovely courtyards, English garden area to grab lunch, easy bus ride to and from the rest of the City.
Oh and Top of the Rock and Empire State are kind of redundant - I'd do Empire State, very late at night, they're open til like 2 I think. You want the lights and it's less crowded.