The gold nanoparticles can be isolated by ultracentrifugation. The centrifugation rate of particles depends upon the particle size and density. If the particle size is known, it can be used to calculate the centrifugation rate. In your situation, if the ultracentrifugation (>150000 rpm) is employed the gold nanoparticles could be isolated.
In addition to Kathirvel's suggestion, you can also increase the centrifugation time which plays a critical role in the separation of nanoparticles. However, this can affect the stability of nanoparticles. So you have to think for an additional stabilizer, e.g. surfactant, sugars, etc, depending upon the application of nanoparticles.
Agree with Antonio. Dialysis is a good method to remove impurities, such as ions, solvents. I used cellulose membrane with cutting molecular weight ~12000, and can purify ~2 nm Ru nanoparticles. You can buy it from many companies. The nanoparticle was prepared in ethylene glycol with polypyrolidone as the stabilizer. Water was used as the solvent in dialysis. It takes ~24 hours to complete the whole process.
It is a good question regarding nanoparticles that is one of biggest questions we have. first you should know whether it is charged or not. If it has a charge by itself or not. Which solvents those particles are in ?
If those particles dissolves in water and it has charge you can use gel electrophoresis to seperate them . If it is not charged you can use sephedex column. If it is not water soluble you have to use either centrifuge systems as kathirvel and jithendra explained or solvent extraction method.