If you want toys not collectables head to the giant toys r us on Odaiba, it is under the big (ocean themed?) shopping centre on there right next to the sega land arcade thing (also worth a visit)
If you want anime style toys you *must* go to akihabara, ignore the big department stores and go in all the specialist preowned collectable stores. Off the side streets of the main akihabara street and down the little covered alleyways. Also go in the big building called radio something with two giant escalators in the middle, the second floor is full of anime and mecha toy shops. Also if you are brave/ can read bits of Japanese look out for signs 3-4 stories up I can't remember the exact wording but it is sometihng like figaa in katakana you will see it all over, head up in the lifts and go to those little treasure troves.
I got some crazy bargains!
If you go near Ueno station there is a giant toy shop just over the road I got lots of cool things from Yamashiroya or similar. It has things like pokemon and hello kitty and other tv characters on one floor, a floor or mecha, a floor of "western" things but tend to be like 80s/90s cartoons things you don't see here (UK) anymore
A floor of girls dolls, pretty much anything!
The ground floor is full of little tacky toy-of-the-month stuff though, like random keychain dogs that sing and are a USB or something so "wacky".. if you are into that kinda thing.
For girly manga and other girl based toys and that go to Ikebukuro it is supposed to be fantastic, but i just found it expensive and full of far too much fan obsessed doujinshi.
As far anime and manga tons of second hand media shops will serve you well, I loved BOOKOFF for dvds but again if you spend time in Akihabara you will find plenty of good cheap anime/manga places.
Anything really newly released head to to the big stores like yodobashi camera, bic camera etc. They habe big sales and promotions on popular new things.
Infact I know so many places for toys in Tokyo I am going to go get you some streetview locations of my fav shops *runs to streetview for nostalgia times*
*edit*
This guy knows it all!
Toy Shopping Guide Part 1 - Akihabara Radio Hall | Toybox Collection
Toy Shopping Guide Part 2 - Akihabara Area | Toybox Collection