An earlier algorithm for Stokesian dynamics simulation of colloid particles in a fluid bounded by a hard wall is extended to the case when a linear shear flow is applied. The algorithm includes many-body hydrodynamic interactions arising from the shear flow with lubrication corrections for pairs of close particles. The extended algorithm is used to simulate small clusters of particles which may interact with each other and with the bounding wall through model potentials with repulsive cores and attractive tails. The pair problem is studied first, in bounded and unbounded fluid, both with and without pair and wall interactions. The critical shear rate necessary to break a bound pair is determined for a range of initial configurations. Whereas in unbounded fluid a bound pair rotates with the vorticity of the shear flow, near a wall the hydrodynamic forces introduce a new breakup mechanism in which the pair tilts through a finite angle relative to the wall before separating. This tilt mechanism requires significantly stronger shear fields than are needed to separate a pair in unbounded fluid. Linear arrays of particles as well as examples of 2- and 3-D bound clusters are studied next to show how the wall and the tilt mechanism modify the shear-induced breakup. With a wall potential included, significant changes are seen in the final distribution of particles resulting from cluster breakup.