Both of those clues work. I especially like “Federations Foes”. For a harder clue, you might want to try something like:
“Enemies of Enterprise”. That way, the puzzler will have to realize that “Enterprise” refers to the Star Trek ship, instead of business, and then know that the Borg are one of the villians in Star Trek.
“Borg” is always in the singular. There are no “Borgs;” there is only Borg.
If this is supposed to be cryptic at all, I suggest something like “single-minded cubists.” Playing on both the collective nature of the species and its preferred mode of transport.
“Federation Foes” would be incredibly vague, because that could be any number of enemies…Romulans, Borg, Dominion…Borg are the only four letter ones I can think of, but I like the “Like-minded Cubists” one.