Some people prefer the downtown area as they prefer to have everything within a short distance. There are many great businesses in the downtown area, as well as a beautiful city park that has live shows and movies througout the summer, and the Big A sponsored car shows which draw large crowds.
Then there is the Township - most homes have larger yards and that country feel, yet close enough to enjoy the city conveniences.
The decision is yours - I suggest you drive around the both the city and the Township and get a feel for what area you like best.
If you would like a list of the homes in the Flushing area, e-mail me at email@example.com and I would be happy to assist you further.
The best thing to do would be to look up the schools in the area and see how they rank. Also, call the local police or sheriff's department and ask about crime rates in the areas.