Hi,
If you're after a one-stop shop till you drop 
place then I would also recommend the Nakano 
Broadway Center. Particularly as it has a number 
of dedicated cel shops.
It is also the main Mandarake store and there are 
a ton of other anime goods/ 2nd hand cd stores 
etc.

To get to the Nakano Broadway Centre.
1. Take a train on the Yamanote line to Shinjuku.
2. Get off at Shinjuku and switch to the JR Chuo 
Line heading towards Nakano. I think its platform 
four but am not certain about this.
3. Nakano station should be 2 stops away. Do NOT 
get off at the Higashi-Nakano station before. It 
is possible to get an express that will bypass 
the Higashi-Nakano station. Just get off at 
the 'Nakano' station.
4. When you arrive at Nakano station, go out the 
North exit.
5. You will be looking across a pedestrian 
crossing towards the entrance of a long covered 
mall tunnel.
6. Just go across and walk through the mall 
tunnel until you reach the other side which will 
be the entrance to the Nakano Broadway Centre.
There are a ton of great shops lining this tunnel 
so its fun to check them out. There is a great 
little stationery shop along there where I buy 
cel books to house all the cels I end up 
purchasing at the centre.
Also, they have some great eating places that are 
reasonably cheap along there too.
7. The anime related shops are from 2nd Floor to 
4th Floor.
Anyway, hope this helps. Have a great holiday!
- X.
ps. Funny thing - on my last trip I bumped into 
Sempei and his friend at one of the cel shops. I 
still regret not buying more Photon cels...they 
were so cheap :(
pps. For other places I recommend Ikebukuro and 
Akihabara. Check out the guide and maps! at 
http://www.cus04.com/guide
Some of the stuff is bit out-of-date. Mandarake 
Shinjuku had closed down the last time I was 
there at the end of March.