Both have deadly weapons, highly trained combat skills and similar views regarding death in battle so they seem like a wash but I lean in favor of the Klingons. The Klingon has a much longer reach than a Samurai and I feel like they can probably withstand greater damage as well. I'm not a doctor or anything but Klingons just seem heartier than humans. More lean meat and bone. The Samurai were, under the code of Bushido, limited to fighting "fair" thus would not likely compensate for the physical handicap with tactics more fitting a Ninja, who would of course, obliterate a Klingon.
I'd give 3 to 1 odds on the Samurai and take everyones money.

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