As the title says, simply, can I use the 3.3v and 5v power pins on the GPIO connector as the reference voltages for a level shifter, or do I need some other reference?
"Reference voltage"... do you mean supply voltage?
The answer to your question is: "Yes - you can probably use RPi's 3.3V & 5V supples to power your level shifter.".
The caveat was added because you didn't specify a particular device, and there are many devices called "level shifters".
Both the 3.3V and 5V regulators on the RPi have some "excess" capacity - by that I mean they are able to source more current than is typically used by the RPi, while maintaining specified voltage levels. See REF1 and REF2 for details. Typical "level shifters" such as this one from AdaFruit, and this one from Texas Instruments can be powered from the RPi regulated supplies.
If you want to minimize clutter and wiring, you may prefer a level shifter that operates from a single supply (e.g. 5V). The Texas Instruments part linked above is one example of a single-supply level shifter.