Doubt it. The WW2 vets showed atleast as much skill and are obviously physically superior. Steel katanas won't fare well at all against the Cap's shield. In fact, in a head-on collision the sword might shatter.
The Winter Soldier seems just as good as the ninja, only with stats to match Cap and a bionic arm to boot.
Once they close the distance the ninja will be overwhelmed in close-quarters due to the bionic arm, shield, and superior stats. Otherwise they are pretty even in fighting skills.
It's a good fight but the Marvel crew is superior, methinks.