Cost wise, there's gonna be a difference in interest rates....2.8%(new car) vs 4.8%(2nd hand),so the civic is gonna be a little bit more expensive.
Other factors:
1. Warranty - City still got warranty
2. Fuel Economy - City wins
3. Power - Civic wins
4. Handling - Civic wins
5. Size - Civic bigger , but City has tons of room available too
6. Condition - Need to make sure Civic has not been in major accident
IMO, it boils down to your convenience & functionality. To me, the Civic has gotten too big over the years, where the new City has taken the place of the Civic of the 90's. For town driving I'd prefer the City, but for long road trips I'd go for the Civic.
Good Luck deciding..