Two 9 V batteries in parallel
In terms of longevity, the 4xAA solution would be better you have more amp-hours.

I don't know what your motor current load is, but for arguments' sake 100mA.  At that discharge rate a typical 9V alkaline will yield about 400mAH, so you have about 800mAH of capacity.  An AA battery on the other hand has about 2500mA hours (since it's in series, you don't x4).
The bigger problem with using 9V batteries at higher loads is that internally they are just a stack of 1.5V cells, so the internal resistance is a bit worse because there are 6 of them to get the 9V.  The only upside is you have a little more margin on the voltage, but at a really high penalty especially on price.

My personal preference would be to use a AA rechargeable system (NiMH), the capacity is almost as good as the alkalines, and you will save money.  Energizer charger/battery packs sell for literally the same price as the rechargeable batteries, so you can buy a couple to swap out if you're running a long time.  You can also add one or two more AA batteries in series if you have the room to give you some margin on voltage.

Just an addendum:

In terms of battery chemistry/technology it depends on what you want your operating cost to be.  Generally I find alkalines to be ridiculously overpriced especially "ultimate lithium" types which are -not- the same technology as Lithium-ion (which is what generally most people are familiar with).   

Lithium ion -is- a good alternative, if you can find a good RC hobby shop they should be able to get something set up for you, but one word of caution- Lithium batteries have very high energy density so make sure you don't get an electrical short.