That's 3 questions! ;)
Here are some answers:
Another question, we will touch down Haneda Airport at 10:30pm, after custom clearance, do you think we still can catch up Tokyo Monorail?
Here is the timetable for the Monorail into town. Based on this, the last Monorail service leaves Haneda around 11:50pm. This should give you just enough time I think. If you don't manage to catch it, there should be bus or taxi services which can take you into town. Haneda is not very far away from the centre of Tokyo, so any extra costs shouldn't be too much (unlike Narita).
What to select in Hyperdia to reach Mt Fuji? There are a few selection start with Hakonexxxxx.
For Mt Fuji, you have 2 destination options: Hakone, or Kawaguchiko. Hakone is further away, but a larger, more Onsen/resort focussed area. Kawaguchiko is also great, and as it is closer is often the starting point for hiking up to the summit.
Both Hakone and Kawaguchiko can only be reached by non-JR trains. However, it is possible to get very close to both using the JR Pass.
For Hakone, you should travel to Odawara on JR, and from there, use the Hakone Free Pass to travel up to Hakone.
For Kawaguchiko, you should travel to Otsuki on JR, and from there use the non-JR Fujikyuko line up to Kawaguchiko.
After I had used up 7-day pass, what card to purchase for going around Tokyo (maybe 2 days 1 night).
The best for Tokyo is to simply purchase a pre-paid travel card and keep topping it up. We have a blog post on these prepaid cards here.
Shall I "keep" one day from 7-day pass for my last day in Tokyo which including heading to airport?
If you are travelling to Haneda, then I don't think it'll be necessary to keep an extra day for use in Tokyo. At ¥620, the Tokyo > Haneda leg is cheap enough for you no to worry about it.
Hope this helps!