You dock between Saratoga Springs and Rainforest Cafe, though the actual entrance into Disney Springs is not by Rainforest, but the next opening down by Eet.
And yes, when I left Tuesday the boats were still not running. Florida is getting good tropical rains the past 2 and next 2 days, but the hardest rains are staying more south - hopefully the central Florida area gets enough to reopen the boats. June is the most common month for the Springs boats to shut down due to low water levels.