OK. Let's take a different tack on this then...
Is the noise present when your stoker stands and pedals out of the saddle? If not, it's probably the saddle to seat post connection. Take it apart, clean and then reassemble using Loctite and set to the correct torque. But, while you're at it go ahead and do the same thing to her handlebar interface with the stoker stem, the mid-section of the stoker stem if it's adjustable, and the clamp at your seat post. No sense in leaving that stone unturned before getting into the drive train.
If there's still a creaking noise when stoker rides out of the saddle and it's only on the right pedal stroke, check the chain ring bolts and make sure they're all snug.
If that doesn't solve it you have two other places to look, assuming you've already addressed the pedals:
- One is the rear hub. If it hasn't been serviced -- and most of them are easy to service -- pull the cassette carrier from the hub body, clean, lube and re-assemble. If it's a White Ind hub you'll need to loosen and then re-set the pre-load cap. DT-Hugi just pull apart. Those are the only two that come to mind at a modest price point that will sometimes have that kind of a noise. DT's more so than White Ind.
- The other is the bottom bracket and, yes... If you don't have self-extracting bolts then you'll need a crank puller or you can simply replace the crank bolts with self-extracting bolts and pull the crank that way. Could just be the crank to spindle interface. ISIS and other splined interfaces are very prone to creaking after X-amount of miles. Square taper can also get that way, which is why it's always a good idea to service the bottom end of your tandem every few years / few thousand miles. Bear in mind, different types of bottom brackets require different types of cup wrenches so it may be more cost effective to pay a trip to the LBS where they'll have all of the various different tools that might be needed.