Official GS boutiques will have the most inventory and also carry the boutique exclusives. Wako in Ginza might be worth a visit as part of Seiko history/lore. You'll also find GS in many department stores. Many department stores will have some sort of 5% off guest card/promo for tourists (separate from and on top of tax free) that you can pick up at a counter before shopping.

If you're looking at the lower end of the GS line (probably mostly quartz and mechanicals with some spring drive), Bic Camera/Yodobashi/etc. may carry them.

Depending on if you care about new in box vs depreciation w.r.t. value and ease of resale, you might be able to find some solid deals at second hand stores that deal in watches and luxury items. The couple times I've purchased second hand items from Japan have all been great, with very reasonable prices and the items in exceptional condition as the collector culture is strong there. This is probably going to affect the quartz GS the most as those generally aren't in high demand if you ever wanted to trade up.