During the past 3 summer, I did my fair share of digging in order to find a decent parcel of sand to lay down on from July to September.
The Hayama beach behind the Imperial Villa (Goyotei) is by far the cleanest and less crowded option that I have found on the Shonan shore. If you want to stay relatively close to downtown Tokyo Hayama is definitely the best option for a quiet afternoon by the seaside.
I have yet to fully explore the Chiba shore before building up a ranking of Tokyo best beaches but for now Hayama will be my summer 2010 number 1 hang-out.