It's all relative. The Leonardos are shops that specialize in buying/selling pre-owned model kits, aftermarket parts, modeling reference books, etc. so while the prices may be lower compared to the States, they are actually overpriced when you compare to other places in Japan. Plus they are located in Akihabara, so you pay the location tax as well. On the other hand, since they are specialist stores, they are good places to go if you don't have the time to look for a better deal on a specific kit.
Meanwhile, Bookoff is a nationwide chain that specializes in pre-owned books, CDs, games, and other media, but has started dealing in hobby items in recent years. Since the staff are not hobby specialists, they often don't know how rare/valuable a kit is and you can find a lot of gems. There will be some damaged boxes or kits that are missing parts/decals (these are generally sold at a nice discount though), but you can always ask them to let you see the contents before you buy (I don't think Leonardo lets you do this). If you don't mind a kit that has the parts bags opened or a kit that is missing the assembly manual but is otherwise complete, or you just need some parts for a project, you can get some great deals.