Multiple Base Excitation in SAP2000

I see that there is a Frame/Cable/Tendon Gravity load assignment which enables you assign different G factors in each direction on a frame-by-frame basis.

Also, you can assign different imposed joint displacements at each support which also opens the possibility of applying time history functions to these displacements.

Both suggestions are admittedly different than using different accelerations at each support, but they may help you get to where you want to go. Let us know if you come up with anything more.