Not sure what part of Tokyo you mean when you say downtown Tokyo but for moving from Hilton Tokyo Bay to Tokyo Station, the process will be:

1. Bayside Station --> Resort Gateway Station (Disney Resort Line, 250 yen, 8 minutes)
2. Walk from Resort Gateway Station to JR Maihama Station (right next to each other)
3. Maihama Station --> Tokyo Station (JR Keiyo Line, 210 yen, 16 minutes)

Going to other places in Tokyo may require another train transfer.