A suica card offers you nothing in savings, but it is convenient to get around and not need to carry a bunch of coins with you to constantly buy tickets. The 7 day JR Pass you can break even on if you use it to go to Kyoto and back, within Tokyo on the Yamanote Line, and to go to Hakone or the Fuji 5 Lakes area. You can also use it on the monorail from Haneda Airport if you arrive at a time when you can activate it there.
In Tokyo the Tsukiji Fish Market is quite an amazing place but if you want to see it, you will need to be there between 4 and 4:30AM to get in line to be on one of the 2 daily tours. The trains and buses are not running at that hour, so if you are not staying close by, you will need to take a taxi to get there (which can be fairly costly). Akihabara is interesting even if you are not shopping for anything in particular. But it won't take you long to look through the place unless you have a big interest in buying some gadget, or manga/anime. To go visit Harajuku to see the youth with their wild fashions, the day to go is on a Sunday afternoon. Meiji Shrine and Yoyogi Park are next to it and well worth seeing also. Be sure not to miss the Shibuya Hachiko intersection especially on a weekend when it looks like half the city is crossing the street all at once. The Sensoji Temple is where every tourist visiting Tokyo goes, and not far from the Sky Tree. Be aware though that the line for the Sky Tree can be long - a weekday is far preferable and you can designate a different time to go up from when you buy your ticket.
For Hakone the Hakone Free Pass can save you a lot of money. Be aware though that one area of it, the ropeway and Owakudani, is currently closed due to volcanic activity. There are buses that will take you around it - but if you had your heart on seeing it, you might consider going to the Fuji 5 Lakes area instead. There are regional passes for both.
For seeing Kyoto, most of the temples/shrines close around 5PM - you could if you still have some energy go visit Dotonbori in Osaka before returning to Tokyo - the octopus dumplings (takoyaki) are famous and it is really quite a place.
In Kyoto you could spend weeks there and not see everything. The three best sights though are the Kinkakuji Temple, Kiyomizudera Temple, and Fushimi Inari Shrine. Fushimi is the most time consuming; you could spend a couple of hours to over half a day if you want to romp over all the trails. You can use your JR Pass to go to Inari Stn to see Fushimi Inari, and the place is one of the few that is free and is open 24/7.
You can maximize your sightseeing time by doing as much train travel at night as possible.
If you have your heart set on going to Disneyland, it is up to you, but Kyoto and nearby really needs more time. Nara is often neglected by some tourists, which is a shame. Missing the Todaiji Great Buddha would be a tragedy. Nara Park has a lot of other great places, such as Kasuga Shrine, Kofukuji Temple, and feeding the many deer in the area. A few other great places missed out even by those who go to Nara though are the Isuien
https://www.youtube.com/watch?v=kk-7IoLELio and Yoshikien Gardens. They are gorgeous and not crowded at all.
A week is really too short, but hopefully you can get a good sample of what Japan has to offer.