If your nanoparticles are magnetically bonded, probably the best way to avoid the aggregation is to use a proper surfactant (perform a search about the best surfactant for your peculiar type of NPs) and then dispersing the solution with a tip-probe sonicator, that applies the power directly into the solution. 

For dispersing the NP's (without any negative effect on the quality of my NP's) I used  to pass the  vial for  2- 3 seconds in the ultrasonic bath. 

Of course as my predecessor said,  the surfactant is very important to ensure the integrity of your NP's. 

You can use bath sonicator for 10s-20s to make it disperse without any major damage to your nanoparticles.

Dear All,

Thanks for your answers, I usually use dextran coated or Pegylated NPS.

as mentioned previously I would use the sonic probe. also add some extra ligand before and during the sonication.