NY - we've taken a 3 day pass (as recommended by Joan L) and plan to do the tour of Downtown, the Night Tour, Statue of Liberty/Ellis Island and the Top of the Rock.

Tokyo

http://www.japaneselifestyle.com.au/tour_detail.php?ProductCode=2142TYO_F880_F830

We've booked the morning tour of Tokyo and a day at Mount Fuji/Bullet Train trip

Hokkaido - we plan to do a tour of Sapporo on foot but we also have a car and driver booked and plan to go to:

Shiraoi Ainu Village, 1 hour south of Sapporo

Shikotsu-Toya National Park, 2 hours from Sapporo

Otaru city and canal, 1/2 hour north-west of Sapporo