You could side-chain it. Personally I'd prefer tuning the Tom. What key is your song in?

Song is in Eb. 

Ok, well it would be helpful to find the EXACT resonant frequency of your tom (it's probably not precisely 100Hz) and tune it to the nearest Eb or Bb.

OK, will try, thanks !  At this point of the learning curve, need all the help and ideas I can get...

Maybe throw the to,s into melodyne to see how they sit with frequencies

Scoot, tlw, Sanderxpander, and everyone else... thanks for the great ideas.  I tweaked the envelope release time a little shorter, AND tuned both racktoms up 2 semitones, and voila !  problem solved.  So it WAS a beating, I guess of the Eb bass guitar and the tom frequencies. The long resonance of the toms just makes the problem periods last longer...   now I can fool with the tuning some more - they don't sound that great tuned up like that, to me anyways, I like the full bodied tone, but may find another lower tuning that works as well.
Thanks again !

Chevy
OK, thanks for the input...  hmmm....   I'm building the song up from drum and bass tracks...  if the bass and drum tracks sound good by themselves, would you proceed with the rest of the song, counting on the idea that the interaction will be sorted out at a later date / mastering / someone better equipped to handle this sort of thing? I'm not familiar with mastering yet, so I dunno.  Or should I keep working at it till it sounds right before proceeding ?  Sort of reluctant to freeze/bounce the whole drum kit, tweak it to perfection via eq and plugins, then realize later that I wanted a change in the drums and have to do the whole thing all over again...   ?

There is no need to worry about this.
 
If you freeze your drum synth you can unfreeze the whole thing with one click, make your edits & freeze again.
 
Just make sure when you do your initial freeze you DON'T include your Fx when freezing.