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Since version 7.6 of Sagemath, there is exactly the required method for Polyhedron objects:

sage: Poly1=Polyhedron(vertices=[[0,1],[1,0],[1,1]], base_ring=QQ)
sage: Poly2=Polyhedron(vertices=[[2,0],[2,2],[0,2]], base_ring=QQ)
sage: Poly1.is_combinatorially_isomorphic(Poly2)

It does not requires the computation of the full face lattice (checks vertex/facet adjacency graph isomorphism), hence should be faster than asking for isomorphic face lattices. The algorithm option can still be set to face_lattice to get another certificate option.