Play with your comp attack time so that the transient gets through and the resonance gets pushed way down. Gating can help too even if you are only gating by 3-10dB.
I tend to like the sound of toms when the bottom head is tuned a half step or so lower than the top head... It kind of creates a downward-pitched "boom" that sounds nice and thick, and it doesn't resonate quite as much as when the pitch stays the same.
I really like evans E-Rings on toms. For less dampening theres an old trick: cotton balls inside the tom, they reduce the ring without changing the timbre.
Honestly, I'd just fade that shit out, or use a gate if I'm feeling lazy. Total control of the sustain. I'd EQ or compress a bit like a snare to get more attack.