I was living Osaka, Japan at the time this trip. My family plus another family flew in from Canada to visit me at the end of March, and we had a total of 7 people in our group. Our trip was 11 days long, and is basically the classic "golden route" but with Kinosaki Onsen instead of Hakone, and Tokyo at the end of the trip instead of the beginning. It doesn't matter whether you do Tokyo first or last. I recommend this itinerary to anybody who is visiting Japan for the first time.
The overall trip
Tokyo > Kyoto > Osaka (with Nara day trip) > Kinosaki Onsen > Tokyo
Arriving at Narita Airport
Their flight arrived in the evening around 4pm. After I met them at Arrivals, I took them to exchange their JR Passes at the JR ticket office located inside the airport (they had ordered a 7-day JR Pass in advance). The activation date for the JR pass would be the following day, since that would time it perfectly for our return to Tokyo in 8 days.
Getting into Tokyo
On this particular trip, we took the N'EX Express which is a train that goes from Narita Airport to Tokyo. We got off at Shinagawa station since that's where our AirBnB was. It's a pretty comfortable experience, costing about 3000 yen for single-way or 4000~ yen for round-trip.
HOWEVER, these days I usually take the cheap airport bus (called the Access Narita bus) instead, since it's just as comfortable and doesn't take much longer. Don't get it confused with the "limousine buses", which cost much more than the Access Narita bus. For those who are concerned that this is a budget option, don't be! The Access Narita buses are no different from the limousine buses. Only difference is that it only does the Narita <> Tokyo Station route and you may need to transfer, while the limousine buses go to a number of different places.
If you are staying in an area that has a direct limousine bus route, I would recommend spending extra for that, especially if you have more luggage. I usually pick accommodation near Tokyo Station on my first night, which is why the Access Narita bus is perfect.
Accommodations (AirBnB in Shinagawa)
Note that AirBnB is only legal in Japan if the host is licensed. Their license number will be listed on the actual AirBnB listing, so make sure to check. Most AirBnBs in Japan are pretty "commercial" and the host is generally not the person whose photo is on there but a management company.
AirBnBs are usually the most value for your money, but you have to put a little more effort into selecting the best one. Hotels rooms in Japan are usually tiny, as in, you will barely have space to open up your suitcase. I almost always stay in AirBnBs unless I'm going somewhere remote.
On this trip, I booked an AirBnB near Shinagawa station because Shinagawa station is a shinkansen (bullet train) stop. I knew that the following day we'd be headed to Kyoto via shinkansen. Alternatively, I could have booked something near Tokyo station but with our large group of 7, I could only find something in Shinagawa.
Departing for Kyoto from Shinagawa station via Shinkansen
We headed to Shinagawa station early in the morning around 6 or 7am. I went to JR manned ticket counter to reserve seats for our group since everybody except me was using JR Pass. Note that unless you have a "Green" JR Pass (premium seats), you are not required to make seat reservations. You can just enter, board one of the non-reserved cars, and sit on any empty seat. Seat reservations should be made when it's busy, such as Japanese holidays. On this particular trip, we did have Green JR passes, so we had to make seat reservations.
Side note on "Green" JR Pass
Honestly, not worth it. The regular seats on the shinkansen are so spacious anyways, I really don't think it was worth the extra bit for the Green pass. If you have the money to throw around though, by all means give it a try! The seats are a little bigger, and there are less people/kids if you want a quieter environment.
We returned to Tokyo from Kinosaki Onsen around 4pm. Basically just checked into our AirBnB for the day.
Day 9 and Day 10
We did general sightseeing in Tokyo for these two days. What you do would be heavily dependent on your interests. A tip is to make sure the places you're visiting in the same morning or afternoon is geographically close by.
We were there during cherry blossom season, so we checked out Ueno Park to see cherry blossoms.
Here are some general places you can look into:
Imperial Palace: Smack in the middle of the city close to Tokyo station. I have never been.
Shibuya: For your shopping needs and if you want to see or experience the Shibuya crossing. Meiji Jingu is also nearby.
Harajuku and Omote-sando: Very close to Shibuya and you should definitely do it on the same day. I would recommend avoiding Harajuku on the weekends since it's a very popular destination for young Japanese people. Unless you want to see the crowds I suppose. Omote-sando is a very trendy and luxury area.
Ginza: Putting Ginza here even though I never really enjoyed going to Ginza since it's so fancy there, but Ginza is like the mature older sibling of Omote-sando. Whereas Omote-sando is where the young rich Japanese go, Ginza is where the older rich Japanese go.
Shinjuku: A very business-y district. You'll find that a lot of hotels and AirBnBs are located here, and I often book to stay here since transportation is pretty convenient. Sightseeing wise, there's really not much here.
Akihabara: On the opposite city of the city from Shinjuku and Shibuya. This is where you'll want to go if you love manga and anime. Go on the weekends and the streets will be closed to vehicular traffic. If you like manga and anime but don't have time/are not dedicated enough to make it out to Akihabara, just google an "Animate" store (chain store for anime/manga) and it'll probably be fine, especially if you're looking for merch for more recent series. If you're a die-hard fan, you should probably go to Akihabara.
Sensoji and Tokyo Skytree: These two are geographically pretty close by. If you want to visit both, definitely do them right after each other. Sensoji is a pretty shrine and there's also a shopping street with traditional souvenirs in front of it.
Odaiba: A man-made island to the south of Tokyo. It's where Comiket is held twice a year. There's a big shopping mall here, a giant Gundam statue, and an onsen theme park called Oedo Onsen Monogatari, which is a pretty fun experience. It will get pricy though. Odaiba has a very futuristic feel, and I loved walking around at night because there aren't really any residential areas there so at night it's very empty. Feels like you're in the future.
Tokyo Disneyland and Disneysea: Regretfully, I have yet to visit either of these. What I've heard is that if you had to choose, Disneysea is more unique to Japan and more suitable for adults.
I dropped the group off at Tokyo station Access Narita bus station and they headed to the airport by themselves. There's a lot of great shopping and food to be done at the airport too!