Eating mostly vegetable matter, and being a rodent, like rabbit, I would think that squirrel would be similar in taste and texture (except red squirrel which also eats meat). I would also expect it to be very lean.
For the above reasons, I agree with Andy M. I might dust with Old Bay seasoning while it's cooking. Are you making a meat and seasoniings type of chili, or a more eastern style with lots of beans, tomato, onion, celery, etc.?
And if the squirrels are with bone, I might just cut it into pieces and leave the meat on the bones. They would add to the flavor. On the other hand, as they are small bones, they might be irritating to the people eating the squirrel. Remove the bones.
The meat may have a gamey flavor, which would go very well with a chili that's seasoned with plenty of cummin, coriander, and some cilantro, as well as chili powder.
I'm sorry. I'm thinking about this as I'm typing. I hope some of what I've said makes sense. I'm quitting now.
Seeeeeya; Goodweed of the North