We are going in a couple weeks and already have a bunch planned, but keep the suggestions coming.
We bought the New York Pass (
http://www.newyorkpass.com/En/) which gets you for free into a ton of places. We plan on biking around Central Park, seeing some of the museums (MoMA, Natural History, The MET), and a few other things. It'll be nice to have so that if we're walking around and see something we want to do, there's a good chance it'll be part of this pass as it has 80+ attractions.
I've heard the Grimaldi's suggestion a few times so we'll definitely hit that up. Big line ups? What kind of pizza should we get?
Are there other things to check out in Brooklyn?