Kameido Tenjin (Shinto) Shrine is a beautiful shrine/temple near SkyTree. Its main appeal is the wisteria garden around a manmade lake. This shrine is less than 15 mins by foot from Kameido or Kinsicho JR stations.
If you visit Tokyo area and want a guide on lesser-known tourist spots to visit, you can check this place out.
The entrance fee is free and it is not so crowded most of the time. It has a very beautiful view of the SkyTree tower.