[Nagoyankee]

Midoriyama: If you're going to be based in Yokohama, what you described may be the way to go. But Midoriyama is easily accessible from Tokyo as well. Take the Denen-Toshi Line at Shibuya (a major section of Tokyo) and get off at Aobadai. From Aobadai, take the bus to Midoriyama Studio City. It only takes 30 minutes one-way (train + bus together).

Muscle Park: Take the Rinkai Line at Shibuya and get off at Tokyo Teleport. It's an 18-minute ride. Then walk 5 minutes to Muscle Park. No transfer needed.

Staying near the Haneda Airport is not recommended at all for a tourist. It's surrounded by big warehouses, factories, highways and polluted rivers/canals. Mostly airline people stay in the few hotels that are there. There are very few stores, restaurants, bars near the airport. It's just dead at night. You will be bored.

You may want to look for a hotel in Shinjuku, Shibuya, or Shinagawa for your purpose. Of course, Yokohama would be a good choice as well.