We have found that when the weather is nice the water taxi is a fun summer option. Our visitors get to see midtown, Chelsea, the village, downtown, the Statue, and the Brooklyn Bridge. Its a view that you are not going to get from a subway.
But even when its just me and my wife, weve found that the water taxi can make for an enjoyable afternoon. One Sunday we started at the Seaport and went to the Fulton Ferry stop. We ate brunch at Bubbys then had some delicious peaches and cream ice cream at the ice cream shop right near the ferry stop. Then we jumped back on the ferry and went to the Chelsea Piers, where we had frozen daiquiris at that Frying Pan. That day they had a live Brazilian percussion band, which played as the massive Norwegian Dawn cruise ship sailed out to sea.
Pros: nice views