We got a Batobus pass for our last day (of 12) in Paris years ago, and spent most of the day plying the river back and forth, getting off for walks and revisits to places we'd liked. It was a nice way to end a long visit, but as Dean said it isn't fast and there can be long waits for the boats.
I'd definitely recommend a boat ride as part of your visit, if the tour doesn't include one. The narrated cruises (Vedettes du Pont Neuf, Bateaux-Mouches, etc.) tell you a lot about what you're seeing, while the Batobus is just a bus that floats. I'd suggest Metro or regular buses (you know, the ones that run on streets) for actual transportation. Metro is usually fastest, but the buses let you see a lot of the street scene, which in Paris can be fascinating. In case you were considering the hop-on-hop=off street buses, I'd suggest not using them because they're slow. If you know where you want to go, just go there. ;-)