It's probably the tranny mount. The stock rubber mounts take a **** quite often, especially on LT1 cars where the rubber is old and has seen a lot of **** over the years. Mine was totally shredded in half- it would thud like 20 times in a row during acceleration. That was pretty damn scary, I thought I'd dropped something in the tranny itself. A polyurethane mount would be the strongest choice, but you may see some vibration from it. I've found that the best choice is the 1LE tranny mount, but they're pretty hard to find nowadays.
To check the mount, just use a jack to support the tranny and drop the crossmember. You'll be able to see if the mount has a crack in it. Although it doesn't sound like yours is totally shredded in half since it's only one thud.
That's my guess, but it could be something different altogether. The only thing that rubs me the wrong way is the fact that you said it happened right when the tranny shifts. Does it happen only when the tranny shifts, or does it happen during heavy acceleration also?