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I'll post this on the travel board at some point too but I know there's quite a few of the Hawaii Nesties that have lived and traveled to Japan before....we're going to Tokyo in early April for a wedding. We want to spend as little time in the city as we have been there before. After the wedding festivities, we'll have a week or so to travel around. Any suggestions for where to go if we want to see the cherry blossoms, a hot springs, and some monkeys? Oh and a ninja museum. In no partifular order

TIA!
Re: Japan Travel Tips
Aaaaahhhh! So jealous! That's the time we went last year and it was AMAZING. So freakin' beautiful. Definitely go to Ueno Park for cherry blossoms. It's super crowded but there's food vendors everywhere and it's just a cool atmosphere. It's supposed to be the most famous place for viewing cherry blossoms in Tokyo. I really loved Kamakura, too. They have that whole street/walkway thing that is lined with cherry blossoms. It's so pretty. I think you can see the snow monkeys in Nagano and there's onsen there, too. We didn't go but I wish we had had time to go there. Otherwise, Hakone is also known for onsen.
Have fun! And take lots of pics! I can't wait to go back to Japan. I was just looking at some photos the other day and longing to go back.
Nikko is a great day trip from Tokyo! I totally recommend that one.
IMO, the best ninja temple (aka: ninja-dera or Myoryuji) is in Kanazawa, but that's a ways away from Tokyo.
The onsens in Nagano (and Gifu - which is where I lived) are AWESOME. One of my favourite places to visit up there is Takayama, which is also known as little Kyoto. It's a great place to walk around.
If you just want to see monkeys, and you're heading south, there are some on Miyajima which is an island off of Hiroshima. They're scary though!
Alyson & Phil | Planning Bio | Married Bio!
Dates & Quinces Blog
I've only been to Japan once about two years ago, but I second kaesha's recommendation for Takayama. Such a cute little town to walk around with cute little shops. I also second Miyajima, but that might be kind of far.....
I'ts been over 13 years since I lived in Japan, but I lived in Nagano and yes they have really awesome onsens. Can't recommend any, unfortunately, because I'm sure it has all changed and I can't remember any.
But they do have a shinkansen to Nagano which makes getting there relatively easy. While I lived there, I did visit Nara and that was really cool to see all the old temples and deer. Have fun planning your trip!
Alyson & Phil | Planning Bio | Married Bio!
Dates & Quinces Blog
I have been to an onsen in Hakone, but I honestly can't remember the name or anything. I do remember that it was really nice and very relaxing! Nice atmosphere there. Sorry I can't be more helpful, my Japan trip was a blur (for many reasons) for me!
Japan in the spring...you lucky girl! It's been almost six years since I was last there and I want to go back - desperately. Are you planning on getting a rail pass? If so, then I think Kyoto would be an great place to see cherry blossoms. Head towards Arashiyama. Not only do sakura trees line the river and cover the hills (so pretty), but there's a monkey park in the area. I don't think they're of the Nagano snow monkey variety, but they're still very cute. There's also a ninja museum and a castle not too far away in Ueno (Mie Prefecture).
If you decide to head towards Nagano (where there are hot springs, monkeys, and, presumably cherry blossoms), then I definitely suggest taking 1-2 days to check out Kanazawa. Like Kyoto, it's one of my favorite cities in Japan and it has the most beautiful garden.
I think cherry blossoms should be fairly easy to see in the Tokyo area like Ueno as Christine mentioned.
I don't know of any ninja museums but there is a "trick" house in Osaka (near Nijo-jyo) where there are trick doors and secret ceiling rooms where body guards would hide. It's in the Lonely Planet. I think there was also a better, bigger house in Kanazawa somewhere-sorry I'm drawing a blank. Probably in the Lonely Planet.
For hot springs, I definitely recommend Hakone. You can buy a Hakone Free Pass in Shinjuku and take the Romance Car all the way there, then do all the stuff included in the pass (cable car ride, pirate ship ride, etc). Izu is another option for hot springs.
If YH reads Japanese, rakuten travel is an awesome website with great deals on hotels and ryokans. You can see pics of the different hot springs for each ryokan in Hakone.