Instead of circle line, opt for the Staten Island Ferry. It only cost 50 cents or so the last time I took it (2-3 years ago), and you can see the statue of liberty (kinda far, but there) and lower manhattan, and all kinds of freaks on the ferry itself, which is always entertaining.
For a fun (but small) museum, if you have time, go to the American Museum of the Moving Image in Queens. You can make your own stop-frame animation, edit a movie, dub your favorite lines from favorite films, play around with a blue screen, see some really great old films (they have showings all the time), and some other cool stuff. Also in the neighborhood is the very quiet and beautiful Isamu Noguchi Musuem. Both easily reachable from the N train.
Also, the Coney Island Boardwalk is a great place to go for a few hours on a nice day.