Back story: I have traveled to Japan, on business, a number of times, but it has been quite a few years. Not since '96, if memory serves. Primarily Tokyo, Nagoya, Yokohama, etc. Never really got to spend "tourist time" there. In grad school in '92 I led a delegation of university students from N/S America to a conference in Nagoya and got to do a bit of sightseeing in Kyoto. Taking wife, son & niece on holiday to Asia this summer. Wife & son have minimal travel experience. Niece has zero travel experience.

Situation now: Son is graduating from high school. Cashing in miles/points for a "last family adventure" before he heads off to university. Taking niece along as well, so we will be a party of 4 "adults." I've traveled extensively internationally, and have previously taken wife & son to SIN, HKG, & China (CTU, XIY & PEK). Also taken wife to DPS. For this trip, son requested a visit to Tokyo, and a revisit to Singapore & Hong Kong. I'm fine "knowing" what to do in SIN & HKG, but am less confident about NRT/Tokyo. Not looking for luxury lodgings in this trip, looking more for functionality, convenience, and economy. So far, flights all in are less than $600 in fees, 4 nights in hotel in SIN are free (Marriott reward points), 4 nights in hotel in HKG are <$500USD (Amex pay-with-points). Trying to keep lodging in Tokyo economical so as to devote cash budget to other experiences more memorable than a bed & shower.

Complicating situation #1: Son & niece are avid anime/manga fans, and have developed some expectations about what Japan will be like accordingly. That's a big part of why they specifically want to visit there rather than elsewhere in Asia, or a trip to Europe instead. I am concerned their "expectations" may not be met, as Japan and it's culture is far more profound than anime/manga. I want to satisfy their "otaku" interests, while still exposing them to a good representation of Japan/Tokyo.

Complicating situation #2: As a family, we are big, big Disney fans. About 8 visits to DisneyWorld, one to Disneyland/California Adventure, and a disappointing visit to Disney Hong Kong back in 2009. We definitely plan to hit one of the Disney parks in Tokyo, but struggle with the decision of whether or not to hit both. May or may not revisit Disney Hong Kong, as it has supposedly been improved.

Itinerary: We arrive 21June2014 late afternoon from the USA, and will head to our hotel. Presently planning on Sakura Hotel Ikebukuro, in Toshima-ku, staying in a Japanese style room for 4 with tatami/futon for 6 nights. Kids will love, my wife and my back might not. Depart 27June2014 mid morning for SIN (4 nights) & HKG (4 nights). Will return to Tokyo 05July2014 early evening for a 1-night layover before returning to the USA early evening on 06July2014. Staying in Narita the 5th.

Known interests: Anything anime/manga (Akibihara, park where people go to do cosplay on Sundays - Yoyogi?, etc.), Tokyo DisneyLand/DisneySea, Studio Ghibli museum, Shibuya intersection, possible day trip to Kyoto, bullet train ride (to Kyoto perhaps, or at least within viewing distance of Mt. Fuji), tea ceremony, pachinko parlor, Tsukiji, etc. Somewhat surprisingly, son is not at all interested in Gundam Front Tokyo. Gundam just "isn't his thing."

Questions:
> What recommendations/suggestions might our seasoned Japan hands have for basically a 5-day stay based in Tokyo, keeping in mind half the party are only 18-19 years old?
> Will staying in Toshima-ku be functional/convenient? The hotel is reputedly a 6-minute walk from the JR Ikebukuro station.
> Given recommendations, are there particular days best suited/not suited for particular sights? For example cosplay park (Yoyogi?) on Sunday, Ghibli Museum not on Tuesday because they are closed, etc.
> Thoughts on hitting both Disney parks or not?
> Feasability/thoughts regarding a day trip to Kyoto? "Must see" things in Kyoto in one day if we go?
> Suggestions specific to Narita area night of 05July, and morning of 06July. We need to get to NRT to check in for our flight back to the USA, scheduled wheels up ~5pm.
> Recommendations on getting around. Keep in mind that on my business travels to Japan before, I always had handlers who arranged trains/buses or drove. In most countries I'm experienced and self sufficient in this regard. In Japan I am most definitely not. Advice welcome.

Please try to keep in mind that the "primary" beneficiaries of this holiday are only 18-19 years old, and therefore have interests skewed toward that demographic. For the most part, the wife & I are just along for the ride. Overall, should still be a very good time.

Thanks in advance.