Some dogs do have anxiety issues (all breeds can have this). I have one that does and one that doesn't. Yorkies are stubborn too
From what I have read, you need to socialize him, take him out to as many places you can, show him different places and people.
Next you need to boost his esteem, you can do this by teaching him commands. If he already knows the basic ones, keep going, stimulate his mind, make him learn.
And you need to make the crate a "happy place" - maybe get a kong or a bully stick for when you have to contain him in there.