The integration of silver and gold nanoparticles with graphene is frequently sought for the realization of hybrid materials with superior optical, photoelectric and photocatalytic performances. A crucial aspect for these applications is how the surface plasmon resonance of metal nanoparticles is modified after assembly with graphene. Here, we used the discrete dipole approximation method to study the surface plasmon resonance of silver and gold nanoparticles in the proximity of a graphene flake or embedded in graphene structures. Surface plasmon resonance modifications were investigated for various shapes of metal nanoparticles and for different morphologies of the nanoparticle-graphene nanohybrids, in a step-by-step approach. Calculations show that the surface plasmon resonance of Ag nanoparticles is quenched in nanohybrids, whereas either surface plasmon quenching or enhancement can be obtained with Au nanoparticles, depending on the configuration adopted. However, graphene effects on the surface plasmon resonance are rapidly lost already at a distance of the order of 5 nm. These results provide useful indications for characterization and monitoring the synthesis of hybrid nanostructures, as well as for the development of hybrid metal nanoparticle/graphene nanomaterials with desired optical properties.