There is a large installation along the East River called the Waterfalls (by artist Olafur Eliasson) which is opening today and will still be on view while you are here. The Circle Line is offering free boat tours but they are already completely booked through July 16th so hurry to get tickets:
http://www.circlelinedowntown.com/waterfalls.asp

You can also take some other free boat rides and get great views of lower Manhattan: the Staten Island Ferry and the Governors Island Ferry (one of the Waterfalls installations is at Governors Island). I recommend spending a little time exploring Governors Island as it will soon be going through some major redevelopment. For more info: http://www.govisland.com/ and http://www.siferry.com/

AmyN