Allow me to share my opinion.
For structural point of view, if you want a rigid connection for rigid frame, its preferably best to connect the beam in the column flanges. For frames that do not required rigid connection (i.e., brace frame), its better to connect it in the column webs.
For top most platform or roof beams as mention by eng1nejoe, it is better to place the beam on top of column plate (cap plate). Continuous beam has an advantage in terms of strength and connection is simple.
Another criteria to consider is in construction. The erection should be doable and simple.
Many thanks.