Atami as a day trip from Tokyo is perfectly feasible. Time things to catch a bullet train there and back. Journey time is 40 to 50 minutes each way, but take care to get on the right train. (Many trains don't stop at Atami). See the Shinkansen timetable here: http://english.jr-central.co.jp/info...ble/index.html

The town has a reputation for ugliness. Monster concrete spa hotels that were filled with Tokyo-ites seeking tawdry thrills in the 60s - 80s are now decaying... Having said that, Mrs. jib was always trying to get me to take her to this golf/spa hotel, which was turned around by a dynamic CEO it seems:
http://www.atamigolf.jp/hotel/index.html

You could do worse than spending an afternoon at the museum, heading to the hotel for a spa treatment, dinner and stay. Then back to Tokyo the next day.