How to plan itenary in Tokyo

My family plan our first visit Tokyo in Nov 2016 for 8 days. Would like to visit the below places and needs advice on the travel train pass, if time permit, would like to visit Kyoto & Osaka.
1) Disneyland
2) Mt Fuji
3) Tokyo Tower
4) Tokyo Sky Tree
5) Shinjuku
6) Shibuya
7) Tokyo Station, Marunouchi
8) Tsukiji
9) Harajuku
10) Asasuka
11) Ginza

Based on what you want to see or visit in Tokyo, you should be able to get through all those places in around 4 days (or maybe 5 days if you need longer tome for shopping around Ginza, Harajuku, Shibuya and Shinjuku). By the way, Mt. Fuji is not in Tokyo, it is around 2 hours away from Tokyo, so you might need another separate day to visit that area. And you might be left with 2 or 3 days for either Kyoto or Osaka visit if you wish to. In this case, I don't think you will need any rail passes, just use IC card in Tokyo and buy train tickets if you end up going to Kyoto or Osaka.

You would want one day for Disneyland, and another full day for Mt. Fuji (actually probably going to Lake Kawaguchi area if you want to "see" Mt. Fuji). So that leaves you with all the other places to visit... in 2 or 3 days, depending on what kind of travellers you are (in terms of pace).

You could probably group: Asakusa - Tokyo Skytree - Ginza or Tokyo station into one day, etc.

So, doing a trip to Kyoto/Osaka in the remaining 2 or 3 days sounds a bit tight, though doable, unless you are a fast traveler. It would help if you can get air tickets arriving in Narita/Haneda and departing from Kansai airport (near Osaka), as that saves you the trip back to Tokyo for departure.

- If you are just staying in/around Tokyo, you do not need any nationwide JR Pass.
- If you are doing just "one-way" JR Shinkansen travel from Tokyo area to Osaka/Kyoto, you do not need any nationwide JR Pass.
- Only if you are squeezing in Kyoto/Osaka visit and doing a "return" trip on JR Shinkansen between Tokyo and Kyoto/Osaka, you can consider a 7-day nationwide JR Pass, as it will start to pay off,

If you wanna visit Kyoto, then you will need to remove some Tokyo destinations.

The fish market, tokyo station and Ginza all werent interesting to me. They were good, but the other places you've listed were better.

Mt Fuji for a full day trip, as in a 14 hours day. Make sure your itinerary has slower days before and after.

Asakusa and Tokyo Skytree can go together on same day.
Shinjuku, Harajuku and Shibuya can go together on the one day.