How difficult is it to get in an out of a Water Taxi with a cane and knee problems?
This website has some information that may help you. It could be difficult because you will have to step down into the boat from the dock. It also mentions that the pilot is not allowed to leave the boat so you will have to be able to handle luggage. The article is from 2010 so not sure if this is still applicable.
http://venicetravelblog.com/2010/02/a-warning-about-water-taxis.html
If you are interested in a vaporetto which is more like a water bus, those are more level to the dock and are wheelchair accessible so I would think they would be easier for you to load. This website has information on all the different types of transportation and some pictures.
http://europeforvisitors.com/venice/articles/vi-transport.htm
Getting from the airport to the hotel is only the start of your potential problems. Venice has lots and lots and lots of bridges, many with stairs. And while the boats used on some vaporetto lines (like line 1, the local up and down the Grand Canal) are large with mostly level access from the dock, other lines use smaller boats that can require steps to get on or off.