-You can take the Staten Island Ferry by the Statue of Liberty for free if you want to go that route and it takes less time than the Manhattan Cruise or the Circle Line Liberty Cruises.You the man!! that is awesome info and I love the local insight b/c I do plan to do the whole tourist thing while I'm there, Thanks!!
-Go to the top of the Empire State Building. Buy tickets online BEFOREHAND! You do not have to wait in the ticket line; you get to go straight through security. Central Park is HUGE as you will see. 800 acres...
-Times Square is overrated. It isn't worth the hassle to get there and get around. There really isn't anything to do there.
-Go to St. Paul's...Church is right across the street from the WTC site and didn't have a single window broken or a grave disturbed on 9/11. A freakin miracle. Also, they have the bench where George Washington would sit when he went to church services as President...It was interesting to me.
-Museum of Natural History: use the subway entrance. It is based on donations but the suggested donation is $14. You can also buy tickets online which are $14 plus a surcharge. If you take the subway you use a different entrance and bypass long lines. You could literally spend an entire weekend just in this museum.
-The financial district around Wall St and the New York Stock Exchange is nice to walk around. Battery Park is pretty and at Castle Clinton you can take a boat out to the Statue of Liberty and Ellis Island. It takes a long time to get tickets, go through security, and wait for boats. My suggestion would be to either look at it from the shore or use the Staten Island Ferry instead.
My suggestion would be to start downtown. Umm, once you make it to the Empire State Building, walk up Fifth Avenue, making sure to hit Rockefeller Center. You see a lot of the city this way and most of the touristy stores like Saks, Tiffany's, Brooks Brothers, ESPN World, etc. Once you reach Central Park, you will see Grand Army Plaza and Park Avenue. Walk over to Park Avenue and that is one of the richiest areas in the country and they have some great architecture.