I'd use "was" and I'd omit the comma if just making a statement of fact. I'd use the comma if the context demanded it, for example if I wanted to differentiate them from other passengers. But not necessarily. Context! Context!
I'd probably say "on" and not "onboard".
There's no context for this sentence unfortunately. English depends heavily on context.
I'd imagine the following would be universally accepted as right among native speakers. Surely no native speaker would believe that "There was two people" is correct.
There were two people, a man and a woman, onboard the yacht.
Of course, I mean to speak of native speakers of standard English, not of native speakers of Ebonics and other nonstandard dialects (viz., "We was robbed!").