The boat isn't your only option to get from Epcot to Beaches and Cream. There is a walking path that goes all the way from Epcot to the MGM Studio, right past BC, YC, BW, etc. If the rest of your party has no trouble walking, you will actually get there faster walking than you would taking the boat.
The water level is a problem for the boats that use Bay Lake - the lake at MK that MK and the MK resorts are around. Because it is a big lake, there is no way to regulate the water level amd it changes based on how much or little rain they have. If the water gets too high, the boat floats too high compared to the dock. If the water level is too low, the boat is lower than the dock. A small difference can be dealt with by using portable ramps or "creative" loading of the boats (ie, loading all the ambulatory people first if the boat needs to be weighted down, etc).
The waterways at Epcot, any of the Epcot resorts or the resorts on the waterways that go to DD are actually navigation canals with a series of other drainage and overflow canals connected to them. By opening and closing gates to the various canals, they are able to keep the water level in the navigation canals fairly constant, so water level would almost never be a problem.
In over 15 years of visits to WDW, we've never heard of or seen a problem with the Epcot or DD boats, even in years when we have not ben able to use the boats at the MK resorts.
We have never had any water level problems at the Epcot resorts or the Int'l gateway. Disney controls the water levels in canals in this section, ensuring that the boats remain accessible.
