My wife and I just returned (as in, about 10 hours ago) from Tokyo, and we had a great time. I can't help you on the hotel because we stayed at a DoD-only hotel at Tegenjibashi (Hiroo Station). For sights, though, here's what we visited:
-Ueno Park and National Museum of Western Art -- park was ok, but museum looked interesting. Highlight of the park for me was the memorial to the Shogi-tai soldiers, which I believe was the inspiration for the Last Samurai movie. There's a Matisse exhibit right now (Y1300 entrance fee, we didn't enter since I've seen a great portion of Matisse's works), National Museum (of history? not sure exact name) has an Ancient China exhibit opening in a week or so which looked really good.
-Yasukuni shrine and Imperial Palace gardens -- I wanted to see the shrine because of the international controversy every time the Prime Minister visits yearly since there are WWII Class-A war criminals enshrined there (along with 2.5 million others...), the gardens are a nice walk with some great picture opportunities - don't miss the MASSIVE koi in the moats (saw 2+ ft fish on eastern side south of east gate)
-Roppongi -- we're not the partying kind anymore, but we did visit the Grand Hyatt (of Lost In Translation fame [wear nice clothes]) and also went to the 52nd floor viewing platform (enclosed) at night. The view is awesome at night, and I got some interesting pictures (a lot of back lighting from the glass unfortunately on most). Some very nice (and expensive) restaurants in the area.
-Ginza -- we walked around this shopping district and found a good Vietnamese restaurant. We visited Printemps, a French department store, and browsed the expensive stuff.
-Shinjuku -- train station is interesting enough to merit a visit since it's the busiest in the world (over 2 million per DAY). There are some surprisingly inexpensive but very good restaurants for lunch in the Takashimaya "Times Square" shopping center up on the 12-14th floors.
National Insitute for Nature Studies (Meguro) -- This is a nice nature walk in the middle of Tokyo if you're looking for some greenery and a slew of noisy crows (as well as a crane or two). It's Y210 to get in, but it's a pleasant break from the steel and concrete hustle and bustle.
Senoji and Asakusa -- oldest and most traditional shrine in Tokyo (in the "old" district, not really old construction-wise, just considered that way), the "Thunder Gate" is interesting, and the long shopping stall walkway is fun if always crowded. The actual shrine is worth a look, and there are little areas nearby that are worth exploring as well. Be mindful when taking pictures of the smaller shrines since many are to honor babies that died (you'll see them decorated with baby bibs), and you might annoy the locals by taking pictures.
Tsukiji -- I wanted to get up early and visit the fish market, but my wife wasn't willing to wake up at 5am.
Should be an interesting visit to THE sushi market in Japan.
One word of advice: BRING VERY GOOD WALKING SHOES. You'll be taking the train, but the stations are not well appointed with escalators. Transfers are sometimes 500m away also.
Email me or PM me if you have any specific questions about Japan. I'll be able to provide info on Hong Kong when we go in November, but I haven't been yet.
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