If you want to go natural hot spring,you go to "maenobara spring sayano-yu" . It is in itabashi-ku . You can enjoy open air bath ,dry sauna,steam sauna,too.
Spa Laqua is not exactly an onsen but they have multiple bath and it's a great spa :)
If you can take a day trip, visit Hakone, Atami, or Nikko. There are great onsens over there.