It's impossible to get to all three Museum Islands in one day, and lord knows, I tried. The ferry and boat schedule make it impossible if you want to stay on one of the islands at night, probably Naoshima.  But, you can get to two out of the three. I chose Teshima so I could see the Sanaa museum there and have lunch at the Shima Kitchen and hike around this less developed of the art site destinations.  Without a van or bike, I was forced to hitch, not a bad solution.