Do you have a pee pad in the crate? I have a playpen for Lacy, with her bed, water and food dishes and a UGO potty, and she uses it all the time now when she has to go and she is in her crate. If you don't have a pee pad in there, try one, or try a UGO potty. I use Natures Miracle Housebreaking Spray on the pad, and it has sure worked for Lacy.

I agree that you should never use crate or any kind of confinement as punishment or discipline. Dogs don't understand time out or why they are being "put away", same thoughts on people who stick their dogs nose in their poop when they have an accident - they have no idea why you're doing that. (Not you, just speaking in generalities)
You said you put him in his crate when you want him to go potty?

As far as accidents go, I'm assuming you mean in other parts of the house not in his crate?
Some Yorkies take longer than others to be 100% potty trained. If he has an accident, don't make a big deal out of it, just clean it up well so no scent is lingering. Continue praising him whenever he goes outside.

Our little girl hasn't gone in the house in over 6 months (she's 16 mo old), then last week, she went two nights in a row. She hates to wake us up so it wasn't really her fault. She hates going inside even though we have never once scolded her for an accident.
She is so good that she goes potty in demand outside. If you say "Go potty", she immediately goes, if we said it ten times, she'd force it ten times!
I LOVE these smart little dogs!

P.S. Mia was never crate trained. She slept in it when we first got her, then she got her jaw caught on one of the hinges (shaped like a J), after that, forget it!

When my dogs were puppies I kept them in the kitchen with news paper and or wee wee pads. The kitchen floor was tile so it was easy to clean , every day. They had enough room to play and had water bowl and toys. I was able to work with out worring. They also had their beds. I don't like crating my dogs when I am not at home. Just my opinion. Any tile or easy to clean surface is good.

Tina