Is it better to book a package deal or separate?
Flights - better last minute or in advance?
Recommended attractions
If anyone can help that would be great!

If by saying a package deal you mean hotel included with the flight and everything, then yes, usually package deals are better than separate because you get more discounts. This is sometimes, other times it all comes out the same. You could get some quotes online on hotels and flights and compare the package deals to getting everything separate, it would help.
Flights are *always* better booked in advanced because they come out cheaper. You could book last minute if you love to throw money out to the nice companies. [=D]
Attractions:
The Empire State building
The Statue of liberty
Rockefeller Center
Metropolitan Museum of Art
Times Square
Wall Street
Bronx Zoo
Central Park

Oh, and aside that, don't forget to go to any decent looking pizzeria or food place, they sell good food =] Site that may be of interest to you: http://gonyc.about.com/od/bestofnewyorkcity/tp/nyc_favorites.htm < #7 = food =D

Have a good time!