I'm trying to get a boss to take damage from a bomb being tossed at them. But it's not working, does it need to recognize the bomb as something before it takes damage? Any help would be appreciated.

You could parent a func_physbox to the boss and make it repair every time it breaks, but add a number to a math_counter each time it breaks, and when there are enough bomb hits, you can kill the boss or whatever.

I noticed in that in the finale, the conversion gel pipe has a trigger around it that detects bombs. When triggered, it just tells the bomb to explode, replaces the pipe with a broken version and activates all the gel splatter effects.
So the pipe model doesn't actually receive or register damage; it's all simulated.

I haven't examined wheatley himself closely, but I bet that's what they did there too.

(If you want to see for yourself, just decompile the map with BSPSource.)

As far as I can tell, there might be a damage_filter_type involved. But I am still having issues.

Edit: Still having issues. This is the only issue that is keeping my map from being released.

For all tubes you break with bombs in the campaign Valve used trigger_once. They used a filter_class_name with the prop_futbol_explosive. If it's in the trigger it fires whatever explosion or damage output. To get the bomb exploding being inside the trigger volume just fire the output "OnTrigger !activator explode".
Make sure to set the flag "Everything" in your trigger_once/multiple.

Well, I'll try to use a trigger to help damage the boss but I don't know if it will work or not.