Efficient Algorithm for Generalized Sylvester's Equation
Here is a paper that addresses the problem you are looking at http://www.sciencedirect.com/science/article/pii/S0096300308006693 It uses Global FOM/GMRES, a generalization of Arnoldi process applied to blocks of vectors using a different inner-product.
It requires A and B to be sparse, or operators for which fast products are possible.