Central city to central city = Shinkansen is the way to go.
Shinkansen is most convenient. Domestic flights can be cheaper, especially if you use a low cost carrier (LCC), but not as convenient. Cheapest is overnight sleeper bus, as the ticket is cheap, plus you don't have to pay for a hotel that night.
Thank you all for the tips.
Just a thought....
If your departure flight back to Sg is from Haneda, why not stay in Osaka for the 1st 5 days and spend the last 5 in Tokyo ? This way for your return home trip you wouldn't have to make such a long way back to Haneda from Osaka - which means that you wud hv to check out frm your Osaka hotel quite early to make up for the traveling time and also the checking-in at the Haneda airport ?
From Central Tokyo area to Haneda, by train, is only abt 45 mins or less. You can then maximise your last day stay in Tokyo and not have to rush so much to catch the return flight home.Edited: 07 June 2018, 23:52