One thing to consider is the coating house’s experience level. Developing solid procedures and processes for conformal coating take time and experience. Many new vendors claim to be able to apply conformal coating as well as the experienced guys, but fall short whenever they run into issues they do not have the experience to troubleshoot. It will be tough to get referrals from your coating house, as a lot of times they are required to sign a non-disclosure agreement. A good way to evaluate their experience level would be to ask how many years they have been in business and their typical weekly, monthly, and yearly volumes processed. A visit to their facility, if warranted by the volume of the project, should give a good indication of the seriousness of their abilities.
When considering possible conformal coating vendors, it is a good idea to look at the types of conformal coating they offer. Some only offer liquid conformal coatings (acrylic, urethane, etc.), some only offer parylene, and some offer all types. It would preferable to select a vendor who offers all varieties of conformal coatings. These types of vendors will be able to direct you to the material that best suits your needs, not necessarily just the types they offer. Also, their experience with multiple mediums will ensure that they are ready to handle whatever surprises may arise during the coating process.
Another factor to consider is proximity to your manufacturing division. A lot of manufacturing has been outsourced and it is often not cost effective to ship product back to the US to be conformal coated. If this is a concern, look for a company with global reach to suit your needs.