Im no expert on 2nd generation Neons, but I would imagine the fuel tank has to be dropped down. Thats how you replace the fuel filter/sending unit/fuel pump. And this type of job can be done by most any automotive repair place - that would have lower prices than a dealership.
Its rare for a fuel pump or filter or pickup assembly to go back on a 3 year old car. After 10 or 15 years you expect it, but not on a car only 3 years old. It would be worth having the dealer do it onl if the work was covered by warranty.