Although most installation instructions don't specify using mortar under showers, many (good) plumbers do place a bucket or two of mortar under the shower base for the reason you are finding out. I agree, you'll have difficulty getting much mortar under the base from the drain hole. What about using a drill bit or small hole saw and drill a grid pattern of access holes under the shower base and either fill them with mortar, or even expanding foam?

Thanks for the response formulaross.
Unfortunately, I only have access to the cut out for the drain. This shower is on the second story and I had to cut a hole in my kitchen ceiling to get to it. I really don't want to cut more holes in the ceiling if I can help it.
I think the expanding foam would crush down after awhile.
I wonder if it would work if I rolled some mortar in a ball and wraped it in newspaper and tried to push/shove it under the shower as far as I could? I'm open to any ideas.
Thanks

Are you sure there is not mortar there now? The crunching noise is common for a job in which mortar was put under the base. Over time, it can crumble a bit and make those noises.

I can see a few inches all the way around where the drain cut out is and there is nothing there. I can get my hand up in there and feel around - nothing there. It definitely is the shower stall, fiberglass crunching sound.

If you have a hole already...you should be able to remove the drain fittings from the bottom of the shower and remove the trap. This should give you adequate room to use your hand and pack in some mortar. Make a bit dry (just enough to mold in your hand...like the consistency you would use for a mud bed in a bathroom) and keep packing it into the void while pushing it back to fill the most of the underneath of the shower.