I've gotta say that Indy wins these. He just has more focus, and I don't think that we've ever seen Jack "bloodlusted." I mean, he just literally drops into situations where he has to surrender or fight, and his fights are based on luck - that's the Jack Sparrow we all know and love.
Plus there's the fact that Sparrow isn't exactly careful with artifacts - where Indy would be "THAT BELONGS IN A MUSEUM!!! RAWR!!"
Indy's fought on ships before, quite a few times actually. I definitely think he's got this.
Jack fought pretty evenly with a centuries old pirate lord, and is probably one of the most skilled combatants in the Pirates verse. Considering he's fought on even terms with and beaten the biggest and best fighters that universe has to offer.
Barbosa, Blackbeard, Will Turner, Davy Jones, etc...
Jack's also much more in tune with his environment. Seemingly to a Jackie Chang-esque level where he can not only use it to his advantage, but to his opponents detriment.