It is unclear how the polymer matrix

The best route is the chemical functionalization of nanoparticle or grafting chetating agent into polymer framework

Dear Pinar, it depends on how the NPs are stabilised. Is it charge or sterric (polymer). If it's charge, try varying the ionic strength of the solution. Generally try and operate at lower salt concentrations. If the NPs are stabilised by polymers, changing the solvent system can help. Finally, aggregation is dependent on the NP number density (or concentration), so reducing the NP concentration can help.

Depending of the type of particles and polymer, clustering can be influenced by many properties, as concentration(particle:polmer:solvent), type of solvent, time/velocity of drying the composite material after blending etc. The best thing you can do is to test the tunable parameters of your system systematically and analyse with e.g. X-ray scattering, if clustering occurs under the choosen conditions or not. That will give you a kind of a Phase Diagramm, and will show you, which under which synthesis conditions you can prevent this undesirable effects for future.

For your special system particle-solvent-polymer you should ensure that mutual interaction between all 3 components is similar in best case. Even in case of preferential interaction particles with polymer deposition maybe irregular. In case of Hansen solubility parameter are similar for all 3 components there will be a near ideal distribution of nanoparticles in or on polymer.

1. surfactant

2. surface functionalisation

Normally Polymers itself give stabilization to nanoparticles. If you still face the same problem even after polymer treatment  try with surfactant to prevent agglomeration.

Oh well... may different factors could be in play. If you are preparing an edible coating (as you suggested by your key words) the selection of the surfactant could be a problem. I will go for predispersing the particles (Ultrasounds) and the proper (I do not know which one) funcionallisation the nanoparticles to prevent agglomeration. 

It depends on the viscosity of your polymer. For a stable suspension, you have to functionalize your nanoparticles with alkoxysilanes and select appropriate surfactant (from BYK) for uniform dispersion. You can use ultrasonication technique for the dispersion. Create a dispersion in smaller volume of polymer using above recommendation and then mix it in full volume.

Can you provide more specifications of the reaction system? I think if you give more information all colleagues could suggest a more specific/efficient approach for overcoming the nanoparticles agglomeration.

Try to modify the surface of the fillers (using silane coulping agents for example), and use ultrasound in each step of the preparation to reduce the agglomerations.

Thank you for your advice.