Nearest to the Park Hyatt, where the bar you refer to is (if it actually existed, they actually "moved" it around a bit for the movie) is the Shinkjuku NS building. Leaving the Park Hyatt, walk down to the street, turn right and go straight. Just past the Shinjuku Washington Hotel, cross the street into the NS building. There are lifts to the top floor restaurant section. In the interior of the building is also the world's largest clock.

If you cross the street at the intersection right in front of the Shinjuku Washington hotel and walk straight past the Tokyo Metropolitan Government building (which has snack bars on the top floors of the two towers), you will see a number of other high rises to your right. Most of those have restaurant floors at the top as well, you can tell which ones because they have signs outside showing the restaurants.

Easy!

There are high rises that are not quite as high throughout Tokyo with restaurants on top. Virtually all department stores, for example, have restaurant floors at the top, including all the department stores in and around Shinjuku station.