The Celine boutique in Omotesando is closest to Roppongi although Shinjuku isn't that far either! If you want to check out Shinjuku's Celine, it'll be in the mall called "Isetan"!
And yes you can definitely call the boutique first to ask what they have in stock and what specific color you're looking for and if they have it you can definitely have them save it for you. I don't know how long they'd be willing to (like months ahead) but you can try. I just know that short term holding it like a day or two to a few, they're for sure ok with it.
Here's their info:
http://www.sunnypages.jp/travel_guide/tokyo_shopping/boutique_luxury_brands/CELINE+Omotesando/2591
GOODLUCK!