5 days in Tokyo, late June with pregnant wife
 

I often get a wealth of good advice from these forums and hope you can help again. I appreciate your time.
My wife and I (both teachers in our 30s) are traveling to Tokyo, Japan, from June 23rd - 28th. This will be our first time visiting Tokyo or Japan in general. We will be flying from NYC and only have five nights so we will stay in the Tokyo area. We leave for Bangkok on June 28th.
My wife and I love to explore new places and cities and have been fortunate to visit several European and SE Asian countries. Japan has always been very high on our list of places to experience so we want to make the most of our short time. We love to walk and explore new cities and enjoy the culture, people, parks and food of the places we visit. We're not big shoppers or big spenders, but will spend for unique Tokyo experiences. I am a history, comic book and pop culture fan. My wife is an art, architecture, quirky culture, music and dance person.
We were originally planning to go with the flow with most of this trip and let our plans develop naturally, but we recently learned WE'RE HAVING A BABY!!!
My wife will be about 5 months pregnant. We have and will continue to consult with our doctors and will be ready to cancel everything if we have to if any health concerns arise.
Now, I would like to plan a lot more than we originally thought we would. And walking most of the day or staying in a pod for a night or two or eating raw fish as often as possible are out.
Here are a few places I need some help:

1. Where to stay - Are Asakusa or Ueon real options (convenient, safe, good local restaurants) or is Shinjuku the best neighborhood for us to stay?
2. Is a day trip to Mt. Fuji feasible and worth it? My wife wants to check it out but I don't think it's practical. We're obviously not going to do much hiking on this trip.
3. Any suggestions for Tokyo activities to give us a break from walking? I'd like to have an activity or two for each day where my wife isn't walking, like the river cruise.
4. Any other recommendations for our first trip to Tokyo based on our interests, especially traveling while pregnant?
Thank you very much for any help you can provide.

We stayed in Asakusa again for our last two nights (Sunday and Monday just gone) and were really happy to be there. It's charming, buzzy, had a lot more eating options than our first stay there a few years ago. Our hotel, the Richmond Premier International Asakusa was superbly located, we had gorgeous views to the Skytree and Sensoji's pagoda. And the price was excellent (via booking.com).
I didn't like Ueno as a hotel location (different previous trip) as much as I'd hoped, but it was fine.
Shinjuku was also good location, though busy busy busy!

Never felt unsafe ever anywhere, even in areas with a few bars, people get friendly drunk rather than aggressive drunk!!

I stayed in the Ueno area, and -- for my interests -- was very pleased. The other area I considered was Asakusa; I just happened to find something that suited my needs a bit better in Ueno. Although I managed to navigate the Shinjuku area quite well one evening, I would NOT have wanted to deal with the chaos of that part of the city every time I wanted to go to my hotel -- too hectic by far for me! YMMV.

I strongly recommend that you scour japan-guide for information about your options and questions:
http://www.japan-guide.com/e/e2164.html

Enjoy -- and congrats!

It will be rainy season in Tokyo when you visit and it will also be quite humid and very warm which may affect your wife in her state. IMHO hotter than August in NYC. You might want to look at day trip guided tours outside of Tokyo to get you off of your feet. Consider Nikko or Hakone or Kamakura or Izu. I have never done one because I can do them on my own but perhaps it would be more convenient for you. It is however unlikely that you will see Mt Fuji during that time.

<< You might want to look at day trip guided tours outside of Tokyo to get you off of your feet. Consider Nikko or Hakone or Kamakura or Izu.>>

Nikko is up, up, up a hill from the train stations and has a good bit of climbing once you're in the main site. The Toshogu Shrine for Tokugawa Ieyasu is partially scaffolded and requires more climbing. This is probably not a good choice for your wife right now.

Another vote for Asakusa - it's the end of the Ginza line which means your wife will always get a seat when boarding. Getting on at Shinjuku is a bit of a scrum at the best of times. You might want to stop in at any Metro station office to ask for a 'pregnancy badge'. Your wife can loop it onto her bag strap if she doesn't want to actually wear it - seated passengers will be alerted to her condition and someone will offer her a seat if she's standing. On the London underground we have 'Baby on Board' badges - same idea.

Many women are more bothered by heat and humidity while pregnant than the would be otherwise. Even though your stay in Tokyo is short, I find myself wondering whether the two of you would enjoy an overnight trip to Hakone. It will be cooler there, and the onsets might be an attraction as well.

<<and the onsets might be an attraction as well>>

Uh, Kathie probably meant onsens.

Thanks, Big Russ. Auto-correct strikes again!

I don't know if this is worth mentioning but I have read that hot baths (and therefore presumably onsen too) are not recommended during pregnancy, so I would get medical advice on this from your own consultant before planning onsen bathing. X

<<I would get medical advice on this from your own consultant >>

I'd get medical advice from the OB-GYN or an RNP who specializes in OB.

Yes, that's what I meant, the consultant for her pregnancy, who's surely OB-Gyn. They may poo-poo the idea that hot baths are to be avoided, just thought I'd mention it as something to investigate before planning onsen visits. ��

I lives in Tokyo and recommend to stay in Asakusa or Ueno area because you can find many good Japanese restaurants, Izakaya and bars in that area. Also Asakusa is tourist friendly area.

Shinjyuku is, like other people said, too many people walking around and sometimes they get really drunk. One of my frien who was visiting as a tourist was taken bank card when he got drunk in Shinjyuku and he found over $3,000 was taken from his account...

Well I am sure you don't get drunk because you are traveling with your wife! But I think it's better to stay inAsakusa / Ueno area.