We took a water mouse from Port Orleans Riverside and had a great time. You can go down the sassagoula, past POFQ, the old tree houses, old key west and all the way to downtown disney. I loved doing that. I think we rented the boat for half an hour and we got to downtown disney and back. They had told us it would take longer but it was fine.
That said, I do think that the best marinas are on the seven seas lagoon because you can go around through bay lake and by the MK. Plus, we were told the little water mouse boats are set to be able to go faster there. I have rented water mouse boats at the GF and Poly. I liked the GF better - but really there is no difference.