It’s unknown - but they mightn’t have to be free to polish a wand.
The house-elf working in MACUSA isn’t carrying or wielding a wand - he’s given one to polish, with the clear expectation that he’ll return the wands to their rightful owners.
“Owls circulate, witches and wizards in 1920s dress are hard at work. Tina guides an impressed-looking Newt through the bustle. They pass several wizards sitting in a line, waiting to have their wands shined by a house-elf who operates a complex contraption of feathers.”
Fantastic Beasts and Where to Find Them - (The Original Screenplay)
There’s no reason to believe that house-elves might not be allowed to clean wands. They’re not allowed to carry wands, but that’s more likely to mean “carry as if it were theirs” than mean they’re not allowed to touch a wand to clean it and give it back.
The status of American house-elves in general isn’t really clear.
Throughout the movie, we see five individual house-elves. There’s the house-elf working for MACUSA, and there are four house-elves at The Blind Pig - one who serves Jacob at the bar, one who brings Gnarlak a drink, one who brings Gnarlak a document to sign, and one who’s carrying a crate of bottles.
The house-elf in MACUSA is only seen using the wand-polishing machine. He doesn’t speak, or do anything indicating whether he’s free or not. It also isn’t clear if the house-elves in The Blind Pig are free or not. The one behind the bar, at least, seems to have a less subservient attitude towards humans than the British house-elves we’ve seen. He’s impatient with Jacob, and not genuflecting like British house-elves generally do. The Hogwarts house-elves, for example, all bow to wizards. However, the difference in attitudes could possibly be because he suspects Jacob isn’t a wizard.
Though it’s unclear how house-elves are typically treated in America, and whether they’re generally free, there are a few ways we can reasonably speculate. Since, in general, American wizarding society seems to be even stricter than British wizarding society with regard to separation from Muggles as well as the control of magical creatures, it’s unlikely they’d have a particularly more friendly position towards house-elves. It’s still possible that house-elves might be mostly free, but it seems unlikely. In addition, since there are fewer wealthy wizarding families in America, house-elves may be rarer there.