I really don’t know enough about either one to compare, except as I mentioned Jersey City’s closer proximity to NY. Jersey City I believe is loosely Satmar based, while Union City is Klausenberg.
Jersey City is in its infancy, however with grand plans for the future which may or may not work out long term (they’re currently working on forming their own branch of Hatzolah).
Union City is more established, so you get what you see, but no plans I’m aware of for major expansion. The Zehviller Rebbe & Rosh Yeshiva there just passed away, so that might effect its future.
I’d assume rents in both places are low, but you’d really need to do your own checking about everything.