We stayed in Shinjuku at the Century Southern Tower which was so very convenient and wonderfully nice for about $200 a night. The rooms were good size with a nice view and the Shinjuku Station is very close by. If possible, you want to stay on one of the areas near the main loop of trains through the city. Shinjuku is one of those and also is a direct shot to Ghibli. Disney was also very convenient. We did not stay at a Disney hotel because they are so damn expensive and, getting to the Parks from Shinjuku was quick and easy. I would stay there again in a heartbeat.

Also, the hotel is right across from one of the best stores in Tokyo - Tokyo Hands.

Shinjuku is at the top of my list right now for the exact reasons you mentioned. Plus I really want to stay somewhere up high with a good city view. It also might be nice to stay somewhere with a view of the Imperial Palace though. Navigating the Subway system is going to be interesting with a stroller, as I just found out that most stations don't have an elevator. With a one and three year old it just isn't optional though.

I am so glad I've started researching so early because there really is so much to plan. I just got my Lonely Planet guide, but haven't even had a chance to crack it open. I have been reading my Just Enough Japanese book that I bought at Epcot last year, however. Not that I remember anything though.

You know what I love most about international travel research? It's gotta be the mistranslations.

From http://shigetsu.com/e/index.html on free internet:

What the heck does that mean? :p

I like the part about serving the newsboy for free. :evil:

Yes, but it would help my vacation fund if I served him for a fee. :evil:

Attractive, Blond, American - Hai
;)

I hereby declare the LoT's new slogan to be:

Lounge of Tomorrow, where even the travel threads turn dirty.

;)

All thought all threads here were presumed dirty until proven otherwise?

I prefer the term "naughty" to "dirty" - but about Japan, you must visit yakatori alley (AKA Piss alley) if you are staying in shinjuku.

I prefer naughty as well. Naughty reminds me of sexy brits, whilst dirty is reminiscent of crack whores and S&M clubs for me. I'll be sure to visit Piss alley. Sounds like a great place for toddlers. ;)