boat thing is a good call- you can see ellis island and get a good view of the statue (i found ellis island to be more interesting, though)
restaurants.. i recommend Buddakhan.. contemporary asian style stuff. fairly pricey though. can't remember exactly where in manhattan it was.
also i think it was the Marriot which has a revolving restaurant in time square that was fun (apparently the only revolving restaurant in the whole city somehow). its also an excuse to go see time square.
if you have an extra day to spend I highly recommend doing the slice of Brooklyn pizza tour:
http://www.asliceofbrooklyn.com/pizza.html
you have to get a reservation for that, though.. and pretty far in advance i think. worth mentioning anyway. they pick you up in manhattan and this guy Tony gives you a great tour of Brooklyn.. takes you to a great view of the Brooklyn Bridge.. coney island.. and 2 awesome pizza places for both Neopolitan and Silician pizza.
other things i recommend... make sure you take the subway somewhere at least once... eat lots of street vendor food... take your pick of your favorite museum(s) near central park. Virtually any one of them could easily be an all-day thing if you wanted to. and while youre near the park visit the Lennon memorial.
also wall street is cool to visit- its on the way to battery park most ways you go (i think) so if youre going to ellis you can probably walk through it. and you can also visit ground zero while you are there- cant see anything as far as their construction... but still.