Patton Oswalt is definitely going to help on this front. Netflix buys a lot of stand up comedy specials, MST3K would be right up their alley and I'm sure their data is telling them just that.
Netflix just let their MST3K contract expire. They had a ton of episodes on the service and now they are all gone. For whatever reason, I don't think they are interested in a new MST3K.
I'm surprised that Joel couldn't get something going with Hulu though. It seems like they are dying to have exclusive content.