What is the best way to thicken the liquid in this recipe?

If you are making a tortilla filler then you probably don't want that much sauce in the end product, so rather than thickening it you might want to consider reducing the amount of liquid that goes into it in the first place. Peppers and onions both shed water as they are cooked, and canned tomatoes have water as well. You don't want to lose your peppers, so I would suggest adding less canned tomato and substituting it with some tomato paste. How much to do depends on the quality of the canned tomatoes, as there's a big difference in quality out there. You get what you pay for - cheap canned tomatoes have water added to the end product, you'll typically get a thicker result and richer flavor with good canned tomatoes as there's more tomato in the can in the first place. That may be all you need to do.

My go-to thickeners are roux, cornstarch and arrowroot powder. A roux is flour fried with butter which is then added to the dish and cooked to a temperature that activates the thickening properties. The good thing about roux is that you can cook it to different levels to add flavor to a dish, but in this case you don't probably don't want that flavor. Cornstarch is relatively flavorless and needs to be heated to a certain temperature to activate it's thickening properties. Arrowroot is a plant product that thickens at a very low temperature, so you can add it after cooking to warm food and it will thicken it without more cooking. In fact, cooking it too much will break down it's thickening properties. It thickens almost instantly too, so there's less guesswork, you just add and stir until it thickens to the consistency you want. Both cornstarch and arrowroot should be mixed with a small amount of water into a slurry before being added, adding directly in powdered form tends to cause clumping.

Another option would be to add a small amount of gelatine at the end of the cooking process, this would thicken up the sauce when it gets cool, and has nice mouth feel.

So first you could try adding a bit of tomato paste and less tomatoes, or using a thicker brand of canned tomato. Or you could thicken using cornstarch or arrowroot depending on whether you plan to cook the sauce additionally afterwards. Experimenting with gelatine might be more work than you want to do, but it has nice properties.

Cornstarch if you want the liquid to remain at the same level of clarity, potato starch if you don't mind it getting a bit cloudier. I would imagine plenty of other starches such as rice starch or oat starch would also work, but I don't tend to get too exotic about my thickeners. Just don't use tapioca in a savory recipe. That's just gross; it adds a strange, bitter-sour taste.

I tried a couple of the suggestions, but the results weren't quite what I wanted. While it was thickened when cooled, it returned to liquid form when heated. My solution, which I will use for now, was to simply add 1/4 cup rice on top of the chicken, but beneath the tomato, etc. The rice cooked well and absorbed the majority, but not all of the liquid. It became thick enough so as to not drip all over while eating.

Adding an absorptive ingredient - eg croutons, diced bread - into the mix after cooking would soak up the liquids and thus keep them in the dish without giving you a thickened sauce (which might or might not be wanted here).

I too love crock pots and slow cookers, but they do have their drawbacks. I am not a fan of removing the end product to other pans and making a further mess, that defeats the purpose. Looking at the mechanics of the recipe, it tells me that it is a ceramic insert and you are home when you cooking it. (3 hours on high) There are a few tips I have developed over the years to help with such an issue. You did mention you do drain the tomatoes somewhat, I would drain them further. As someone mentioned, you could add a little tomato paste, but not too much.

The problem with adding thickeners in the beginning (outside the recipe) is that you risk deactivating the thickening power, or it thickens too soon and begins to burn on the bottom. There is no accuracy with crock pots and slow cookers.

You can approach this two ways or a combination of the two. If you are present when cooking, I would leave the lid open a crack with a wooden spoon for the last half hour, tilting the lid so the water does not go back into the pot. I usually use a paper towel to catch the water. This ensured the most of the heat is being reflected back into the pot. Using this method you may want to add and addition half hour in cooking. When almost finished you can thicken the liquid with different choices, but it depends on what outcome you are looking for. Is the liquid condensed enough for full flavor? Do you want a clear broth, does that matter? If I were cooking this recipe, I would finish it with Wondra Flour. It is a precooked flour in a can. http://www.goldmedalflour.com/ourflourstory/ourflour/wondraflour Since it is already been activated by the precooking, you wouldn't need a high boil point for it to thicken, mostly time to hydrate. I would start with a teaspoon, then put the cover completely back on and give it an additional 10 mins.

You can also use powdered soy lecithin found in the drugstore aisle where thickened beverages such as Ensure are located. Lasts forever, is tasteless, and can be used at any temperature to thicken vegan mayo and vinegrette, as well as in hot mixtures.