Here is another great trail in the Tokyo prefecture, again near Yokota Air Base, about 35 minutes away. The website below is a great representation of the area and the trail is easy to find as you will see a ton of mountain bikers every time you head up there on a clear day.
The Sengen One trail is an awesome beginner to intermediate trail and very smooth. The area after coming down the trail is also great as their are some waterfalls in the nearby area as shown at the map at the bottom of the trail next to the bathrooms. If you are not up for the ride up the 20 kilometer hill it would be best to either have someone drop you off at the top of the mountain next to the trail entrance or get a bike bag and take the bus to the top of the hill as I did with my son since he cannot yet make it to the top of the hill.