This was my 3rd time staying on the boats! I love it! And the neighbourhood is actually really close to the downtown. The very best thing is using a scooter or a bike to do your day adventures, but the Prague public transit is also really convenient and easy once you learn how to use it.
The boats are a playful sort of accommodation. Not proper for anyone with a mobility impairment, and no good for people that want a lot of privacy. But to me, half of the fun is making friends with the other guests on neighboring boats.