I take my 17 foot canoe in my toy hauler every time but I can't imagine there being enough width for a jon boat or I might be trying that instead. I stack my 12 foot commander kayak on top of the canoe and use a trolling motor with that.
It is the one time not having a separate garage is a benefit.
I would think even with a garage you could just leave the door open and let the kayak or canoe go into the living space. I guess it depends on the layout but I would think most times this would work. Especially if you are only needing 2-4' into the living space.
I put my boat on top of the truck.
I don't have a good picture of the boat trailer, but it is a three piece design. See the second picture, two of the three pieces of the trailer are in the back of the truck.
The toy hauler is used to hall the ATV that I use to two the boat and trailer into remote lakes.