Out of the four films to date, which has the better ending of the two?
I vote KOTCS. Last Crusade's ending is a little too overly cliched, with Indy literally riding into the sunset...A perfect "Hollywood" ending but a little heavyhanded in its message. Before Indy V was announced, I figured KOTCS would mark the last of the Harrison Ford films...As such I view KOTCS as the better ending. It brings the character full circle from the ending of Raiders of the Lost Ark.
If you view the quadrilogy as a saga (which I tend to do), KOTCS is both a perfect epilogue and a good finale. This time Indy truly finally gets the girl. He doesn't come home with the golden idol or the Cross of Coronado, but with a much greater treasure. It works also as a perfect epilogue due to the time gap between Last Crusade (and Mystery of the Blues) and Kingdom - and thankfully, it ends on a much happier note than most other epilogues (such as the story of Robin Hood's demise) do.