Jimmy, I assume that you will do this anyway regardless that you won't see much. If yes, Venice is a bit more expensive than Florence. Other than that, it doesn't really matter. As for the water-taxi, I hope that you mean water bus and not taxi. The vaporetto is the public water bus that has regular stops along the canals. These are quite inexpensive. The water taxi is a private boat much like a taxi. It will take you right to your hotel if its near the water. The minimum fare for a water taxi is 125Euro ($190) for up to 6-7 people. You can do either - just know the difference.
Lastly, do not drive a rental car anywhere in the Florence historical area. Its all a giant restricted zone and they will get your license plate with computerized cameras. BIG ticket. If you don't know what a ZTL is and/or you don't want multiple $150 tickets, don't drive there. The high-speed train between Florence and Venice is far more convenient than a rental car. Its city center to city center.