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Gundamstoreandmore
Something of a joke these days, considering they are out of stock for most new kits and update around three times a year. But if they do have something you’re interested in, it’s well worth buying from them since you can avoid international shipping. Also worth checking out for their weekly and monthly specials, which can be any number of things.
Hobbywave
Flat $12/$18 shipping fee and only for US/Canadian residents are all you need to know. Much better stock than GSAM (including tons of modeling supplies) and they actually update their website fairly often. Cheap prices too, though that’s offset by the shipping. They ship on Tuesdays and Thursdays, and allow you to add items to previous orders if they haven’t shipped yet.
Gundam Planet
Despite the name, they sell a ton of japanese toys. Their prices are pretty in line with Japan based companies. Shipping is either via USPS (pay by weight) or FedEx (pay by order value). Flat $9.99 for Fedex on orders less than $100, maximum of $18.95 charge for orders in excess of $300. Only thing to watch out for is that they will let you order backordered items currently, and they’ll hold your whole shipment until the backordered item is in (generally two weeks). They’ve got a pretty rad website design and open up their location on Fridays, Saturdays and restock days. Last time I went they had a few kits at reduced prices that they didn't put on the site because they came with damaged boxes from their shipment.
HobbySearch
Actually called 1999 in Japan (when you google hobby search, it pops up, it’s the right site). Being based in Japan gives them a massive advantage, the day a kit is released, it’s available for purchase and if you pre-ordered it, they’ll send you the bill. They have standard international shipping rates and the occasional sale on kits or shipping. I’ve had several good experiences with them and they respond well to emails.