Sorry that I missed your transit schedule, arriving at 6 a.m. and departing at 11 a.m. You will be at Tokyo early in the morning.

• Many stores at Ginza do not open till 10 a.m.
  
  
• Tokyo tower opens at 9 a.m. Considering trip back to Haneda Airport, will possibly give you less than an hour at Tokyo Tower. Going through security, departure passport control, then want to be at the gate least by 20 min. before the departure. Question is what to do till 9 a.m.?
  
  
• Hamarikyu park opens at 9 a.m. Same situation as Tokyo Tower.
  
  
• Kawasaki Daishi temple opens at 6 a.m. You will have no problem with Kawasali Daishi.

Because of your early arrival, many places are not open yet at Tokyo. Due to your 11 a.m. departure that makes it tight schedule and not much time at a place you want to visit in Tokyo.