How about a handsome cab ride around Central Park? I bet the wife would love it and I think they only take you around for 20-30 minutes. There are tons of them available on Central Park South.
Times Square is a must. Just to take it in. Buy something off a street vendor, duck into a store that interest you, grab a slice. Whatever.
The ferry idea sounded good. Make sure to visit the WTC site if you get down to that end of NYC.