Hey Achi: I live in Union City and own a few houses here. I would say that, in general, "uptown" Union City is seen as more desirable. The numbered streets run east/west and are numbered south to north (2nd St or Patterson Plank is the southernmost street/borders Jersey City, 49th is the northernmost border with West New York), John F Kennedy is the westernmost border with North Bergen, and Palisade or Park is the easternmost with Weehawken or Hoboken.
Stuff in the 30s and 40s is seen as nicer than below, and it's where most of the highrise buildings in Union City are. 30th St is where the Lincoln Tunnel is, and where all the buses go to NYC, so that's pretty desirable due to its access to New York. The further east you go/closer to Weehawken or Hoboken is also generally nicer: so right along Park Avenue in the north is very nice (borders Weehawken) near the Pathmark supermarket, or along Palisade Avenue in the south. Some houses along Palisade and Park have views of NYC which is obviously very desirable.
I also really like the area around the Monastery (18th through 21st streets between Summit and West)--it's quiet and neighborhoody, or just south on 14th or 15th (also near an old church).
There are pockets throughout the city that are nicer than others, but the only "not as nice" areas are probably in the single digits along Bergenline or West St. Bergenline is the main commercial street throughout Union City and it sort of dies around 14th St, so stuff south of there is not as great mostly because you don't have access to restaurants and the commute to NYC is longer. However, you're super close to Hoboken (can walk to an elevator which takes you to Hoboken and the light rail), and you're bordering Jersey City Heights, which has changed a huge amount in a short time and has restaurants, bars, etc.
In my mind there aren't almost any areas I'd consider "bad" (the whole city is like 1 square mile), but it's very block-by-block, so you'll get a sense when you're walking around.