The last two samurai swords

Masamune: Aquired by stealing them from Marquis Elmdor inside of Limberry. (Along with the Genji stuff)

Chirijiraden: Found on the last level of the Deep Dungeon. (END), along with the Chaos Blade.

Also, high level ninja like to throw the masamune. I am not too sure about the chirijiraden but I am sure they would throw that as well. The best place, in my opinion, to get in a battle with ninja would be the forest after Dorter Trade City. (I forgot the name at the moment, forgive.) If you enter from the Dorter side you have a chance at entering the rare battle with all ninja. It isn't that hard, just have each person you use in the battle have catch and a relatively high brave. I just recently got the true Javelin and three Chaos Blades in that battle. It seems though, at least in my game, that only the single female ninja throws the good items, the rest only throw shurikens and such. Just remember to enter from Dorter, make sure to save there before you go over, if you don't get in the right battle just reset and keep trying, eventually you will get it, and some really rare equipment.
Later.

Only the Masamune stays with Elmdor. The Chirijiraden is in the last battle of the Deep Dungeon, the one with Elidibs (Serpantarius..spelling?) and his Apanda army.

Just remember in the Deep Dungeon, SAVE OFTEN. Because if that rare item turns into a phoenix down you can't go back and try again. (It'll turn into a trap) So keep that in mind while going for the Cirijiridan and Chaos Blade. I happened to miss a few items when i first went through:ashamed: