A topic near and dear to my heart.
I have this info posted on several guitar forums but not here.
In regards to eBay sellers, I recommend people do not use them. I would suggest avoiding them like the plague. 99% of the eBay sellers do not actually own the gear they are selling. They steal the photos from the actual stores that have the item for sale and make the eBay ad. If you win the auction or buy from eBay, they take the money and then go to the store and buy the item and then send it to you. If the store has already sold the item, they make up some excuse to cancel the sale. The price is usually significantly marked up from the retail price in Japan. 30%-60% is not uncommon. For low price items, they sometimes have a better price but I still advise against using them.
If you want something from Japan, I recommend first checking digimart.net. This is the big musical instrument site in Japan where dealers list many of their instruments. Foreigners, unfortunately, cannot buy directly off digimart but it is a good resource to see what is available. For the savvy, it is also good to check the websites of the individual stores because some items are not listed on digimart.
The best way to buy is if the gear you are interested in is being sold by a big dealer. Most of the big dealers in Japan ship internationally. The only caveat is that all have restrictions on selling certain brands new overseas. (i.e. Fender, Gibson, PRS, etc.) No issues with used gear or Japanese brands. It is usually ok for European brands but some restrictions may apply.
You then just need to contact that dealer. The big stores like Kuroasawa, Ikebe, Ishibashi, Shimamura, have a contact page for overseas sales. Just use the form to tell them what you want to buy and they will contact you by e-mail with pricing and availability. This is the preferred method because as a foreigner, you do not have to pay Japanese sales tax (VAT) and can take 10% off the listed price. The price listed in Japan includes tax. They will send you a Paypal invoice and you will have the gear very quickly. Shipping is 2-3 days via commercial carrier with time added for packing.
Aside from the big stores, many smaller stores also ship internationally. Just ask the store. The fore mentioned Geek in Box in Yokohama is a good example for basses. They ship internationally and even sell on Reverb.
If the store that has the gear does not do international shipping or you want to buy a new bass from a brand with restrictions, then you will need to use a proxy service. These have been mentioned in several posts above. These are services that are based in Japan that will buy things for you. You tell them what to buy and they go buy it and have the item sent to their warehouse. They can store items and group them for a single shipment. They then will ship the item for you. There are fees involved but significantly less than the eBay sellers. Each proxy service has their own fee structure, policies, pros and cons. Buyee, Jauce, Zenmarket, Rabbit Japan, etc. are examples of such proxy services. There are dozens and dozens of such services. You could also use re-shippers like Tenso or Black Ship.
The proxy services also allow you to buy from Japanese auction sites like Yahoo Auctions Japan (eBay quit the Japanese market in the early 2000's). You also buy from used goods stores like Hardoff and buy from marketplace sites like Mercari. This is where you can find some bargains. I just won an auction for a guitar last night and I feel guilty how low a price I paid.
Do expect to pay duty if the item is priced higher than $800USD and shipped via commercial carrier. You can avoid duty if the item is shipped EMS but EMS is kinda of slow now and even slower for items like a bass.