We go twice a year. We love it. Our favorites:
walk across the Brooklyn bridge. Stunning views from the middle. Grab a slice under the Brooklyn bridge at Grimaldi's.
9/11 museum. It is a humbling experience. When you're done check out the ellipse (west fields work trade center) across the street
Rent a bike and ride the bike paths along the Hudson River
Grab a deli sandwich and have a picnic in Central Park
Ride the Roosevelt tram
Avoid little Italy. It's not what it was.