You can rent a boat at the YC, but I agree with you that either the Seven Seas Lagoon or Bay Lake is a better place to rent one than at YC. The lakes are more interesting over there.
You can rent boats at several resorts, including the Wilderness Lodge on Bay Lake.
We rented at the YC, but we spent most of our time trying to avoid the boats picking up passengers at the resorts. Once you go by the Swan and Dolphin and go down to HS, there isn't much to see. We had fun, but next time we'll rent elsewhere.
We love renting on Bay Lake and the Seven Seas Lagoon, there is so much to see and you can boat right in front of MK. Our second choice would be DTD or one of the resorts on that waterway, since there is more distance to cover. It seems you can see most of the Epcot area by friendship boat.