Intercontinental Yokohama Grand is not a bad location at all. The hotel is right at the tourist bay area of Yokohama, many Yokohama tourist area is nearby. Plenty of restaurants and shops, including Chinatown. Department store shopping will be 3 min. ride on Minatomirai Line to Yokohama station. From Intercontinental Yokoyama Grand to Minatomirai station is 7 min. walk.

From Minatomirai station, Shibuya in Tokyo is a direct train (no transfer) with 37 min. ride on the fastest limited express train. There are 16 departures from Minatomirai station to Shibuya every hour, and 4 of them are limited express service. Shinjuku in Tokyo is also a direct train service from Minatomirai station, 47 min. ride on limited express train to Higashi-Shinjuku station. Tokyo station, Ginza, Shinbashi, area will require a transfer of train from Minatomirai station but should get there an hour or so. The train between Tokyo and Yokohama is a busy commuter route. Trains are buys all day long, not just during rush hours.

You have visited Tokyo only once when you were little, so it is almost same as the first time visitor to Tokyo. Yokohama is a very nice area, and I have done more than few weekend day trips from Tokyo area to Yokohama, but I have a feeling you will be spending more time at Tokyo area than at Yokohama area. For that reason, I think hotels at Tokyo will be more convenient for your trip.