We never walked (we got plenty of walking in at the parks themselves - Saturday we walked 9 miles and Sunday 7 miles!) but the boats were very quick. Only once did we have to wait for a boat at RPR, most of the time when we arrived at the bag check, there was a boat there, or just arriving) and only once did we have to wait for a boat at Citywalk.
The boat ride itself is almost exactly five minutes once they launch. It drops you off on the other side of the water from both parks - you go left to go to USF, right to go to IOA. From there, it's probably a two minute walk to USF, maybe another minute longer to IOA? There's no shuttle from RPR, just the boat or the walking path. We saw lots of people using the walking path.
We were coming from Tower 3, which was the most convenient for the boat dock. You come out of the elevator, go outside, and the signs to the path were very easily marked.