Hi, Amy!
Yes, those boats at Downtown Disney really do exist! :-)
Take a look at this
official map of Downtown Disney and zoom in so that you can see the lake from one end to the other. Notice the boat docks at DD's Marketplace, Pleasure Island and West Side. Click on the little boat icon and see more information about Walt Disney World Water Transportation. At certain times of the day, these ferries make stops at each of these docks.
There is a great, unofficial, post about the new DD Water Transportation on WDWMagic.com. Just enter "Downtown Disney Water Taxi" in their search bar to find that article. This is a great source of scheduling information, especially now that the dock at the West Side has reopened.
Have a wonderful trip, Amy! Be sure to send more questions as you think of them, too. We love to help!